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Code Issues Releases Wiki Activity

*/*: sync with upstream 

Taken from: FreeBSD
This commit is contained in:
Franco Fichtner 2023-08-11 09:38:15 +02:00
parent 5fab86160f
commit c6b462f216
573 changed files with 5907 additions and 16851 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
archivers/bicom/Makefile
View File

@ -1,8 +1,7 @@
PORTNAME= bicom
PORTVERSION= 1.01
CATEGORIES= archivers
MASTER_SITES= http://www3.sympatico.ca/mt0000/bicom/ \
http://freebsd.nsu.ru/distfiles/
MASTER_SITES= http://www.mirrorservice.org/pub/minix/distfiles/backup/
DISTNAME= ${PORTNAME}${PORTVERSION:S/.//g}
MAINTAINER= ports@FreeBSD.org
@ -15,7 +14,8 @@ LICENSE_NAME= bicom
LICENSE_TEXT= Contact author personally regarding commercial use
LICENSE_PERMS= dist-mirror pkg-mirror auto-accept
USES= zip
USES= dos2unix zip
DOS2UNIX_GLOB= *.cpp *.h
NO_WRKSUBDIR= yes
MAKEFILE= ${FILESDIR}/Makefile

22
archivers/bicom/files/patch-bialib_sufftree.h
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@ -1,11 +1,11 @@
--- bialib/sufftree.h.orig 2000-10-26 01:51:04 UTC
+++ bialib/sufftree.h
@@ -95,7 +95,7 @@ class SuffixTreeModel : public Arithmeti
{
public:
bool InEdge()
- {return(r>0);}
+ {return(r!=NULL);}
//After Canonize()ing a point, r >0 <=> proj!=0, i.e., point
//is inside an edge
INode *ins; //parent of point
--- bialib/sufftree.h.orig 2000-10-26 01:51:04 UTC
+++ bialib/sufftree.h
@@ -95,7 +95,7 @@ class SuffixTreeModel : public Arithmeti
{
public:
bool InEdge()
- {return(r>0);}
+ {return(r!=NULL);}
//After Canonize()ing a point, r >0 <=> proj!=0, i.e., point
//is inside an edge
INode *ins; //parent of point

11
astro/kstars/Makefile
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@ -1,5 +1,5 @@
PORTNAME= kstars
DISTVERSION= 3.6.5
DISTVERSION= 3.6.6
PORTEPOCH= 1
CATEGORIES= astro kde
MASTER_SITES= KDE/stable/${PORTNAME}
@ -10,8 +10,8 @@ WWW= https://edu.kde.org/kstars
LICENSE= GPLv2
LIB_DEPENDS= libcfitsio.so:astro/cfitsio \
libindidriver.so:devel/indi \
LIB_DEPENDS= libXISF.so:graphics/libxisf \
libcfitsio.so:astro/cfitsio \
libqt5keychain.so:security/qtkeychain@qt5 \
libraw.so:graphics/libraw \
libgsl.so:math/gsl \
@ -37,4 +37,9 @@ USE_QT= concurrent core datavis3d dbus declarative gui multimedia \
buildtools:build qmake:build
USE_XORG= x11
# Requires devel/indi >= 2.0.0 which is not in the ports tree yet. KStars builds
# fine with INDI 2.0.3, but support for the INDI 2.0 API in astro/phd2 and
# astro/stellarium as of 2023-08-10 appear to be works in progress.
CMAKE_ON= CMAKE_DISABLE_FIND_PACKAGE_INDI
.include <bsd.port.mk>

6
astro/kstars/distinfo
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@ -1,3 +1,3 @@
TIMESTAMP = 1685647969
SHA256 (kstars-3.6.5.tar.xz) = 1c2a4510f0029e05e0cf3e76d83fabb6cf620165f142f95aad744f89fbaf2eb6
SIZE (kstars-3.6.5.tar.xz) = 114135376
TIMESTAMP = 1690902260
SHA256 (kstars-3.6.6.tar.xz) = 6783dab51bed2090687910c9258924053381fd1f91ee719d0d3dfc6df0128494
SIZE (kstars-3.6.6.tar.xz) = 135870036

54
astro/kstars/files/patch-kstars_CMakeLists.txt
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@ -1,56 +1,26 @@
Patch by Heiko Becker upstream:
Fix linking without INDI
Without INDI present I get the following error:
ld: error: undefined symbol: pthread_create
>>> referenced by __threading_support:378 (/usr/include/c++/v1/__threading_support:378)
>>> supernovaecomponent.cpp.o:(std::__1::thread::thread<io::detail::AsynchronousReader::init(std::__1::unique_ptr<io::ByteSourceBase,
std::__1::default_delete<io::ByteSourceBase>>)::'lambda'(), void>(io::detail::AsynchronousReader::init(std::__1::unique_ptr<io::ByteSourceBase,
std::__1::default_delete<io::ByteSourceBase>>)::'lambda'()&&)) in archive lib/libKStarsLib.a
"x86_64-pc-linux-gnu-ld: ../lib/libKStarsLib.a(robuststatistics.cpp.o):
in function `Mathematics::GSLHelpers::gslMedianFromSortedData(
double const*, unsigned long, unsigned long)':
.../work/kstars-3.6.5/kstars/auxiliary/gslhelpers.h:306: undefined
reference to `gsl_stats_median_from_sorted_data'"
That is the case because Mathematics::RobustStatistics is used
unconditionally, which pulls in gslhelpers and the need to link with
GSL.
Also drop the duplicate linking of KF5::Notifications, KStarsLib already
links to it in the NOT ANDROID case.
--- kstars/CMakeLists.txt.orig 2023-05-31 08:23:38 UTC
--- kstars/CMakeLists.txt.orig 2023-08-01 06:19:45 UTC
+++ kstars/CMakeLists.txt
@@ -1169,6 +1169,8 @@ set(kstars_SRCS ${kstars_SRCS} ${fits2_SRCS} ${sep_SRC
set(kstarslite_SRCS ${kstarslite_SRCS} ${fits_klite_SRCS} ${sep_SRCS} ${hough_SRCS} ${fits2_klite_SRCS} ${kstarslite_libtess_SRC})
IF (NOT ANDROID)
+ # GSL
+ find_package(GSL REQUIRED)
qt5_add_dbus_adaptor(kstars_SRCS org.kde.kstars.xml kstars.h KStars)
qt5_add_dbus_adaptor(kstars_SRCS org.kde.kstars.SimClock.xml simclock.h SimClock)
qt5_add_dbus_adaptor(kstars_SRCS org.kde.kstars.FOV.xml fov.h FOV)
@@ -1213,6 +1215,7 @@ IF (NOT ANDROID)
)
add_library(KStarsLib STATIC ${kstars_SRCS})
+ target_link_options(KStarsLib PUBLIC ${CMAKE_THREAD_LIBS_INIT})
if (BUILD_PYKSTARS)
set_target_properties(KStarsLib PROPERTIES POSITION_INDEPENDENT_CODE ON)
@@ -1243,6 +1246,7 @@ IF (NOT ANDROID)
Qt5::WebSockets
@@ -1250,6 +1250,7 @@ IF (NOT ANDROID)
${ZLIB_LIBRARIES}
Eigen3::Eigen
+ GSL::gsl
GSL::gsl
+ Threads::Threads
)
if (Qt5Keychain_FOUND)
@@ -1313,10 +1317,6 @@ if(INDI_FOUND)
@@ -1320,7 +1321,6 @@ if(INDI_FOUND)
## Linux + MacOS Lite: Requires INDI Qt5 Client
## Android: Requires INDI Qt5 Client built for Android
if (NOT ANDROID)
- # GSL
- find_package(GSL REQUIRED)
- include_directories(${GSL_INCLUDE_DIRS})
- target_link_libraries(KStarsLib ${GSL_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} KF5::Notifications)
- target_link_libraries(KStarsLib ${CMAKE_THREAD_LIBS_INIT})
# StellarSolver
target_link_libraries(KStarsLib StellarSolver::stellarsolver)
endif ()

275
astro/kstars/pkg-plist
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@ -168,6 +168,9 @@ share/doc/HTML/en/kstars/astrometry_settings.png
share/doc/HTML/en/kstars/astrometry_windows_ansvr.png
share/doc/HTML/en/kstars/blackbody.docbook
share/doc/HTML/en/kstars/blackbody.png
share/doc/HTML/en/kstars/build_filter_offsets.png
share/doc/HTML/en/kstars/build_filter_offsets2.png
share/doc/HTML/en/kstars/build_filter_offsets3.png
share/doc/HTML/en/kstars/calc-angdist.docbook
share/doc/HTML/en/kstars/calc-angdist.png
share/doc/HTML/en/kstars/calc-apcoords.docbook
@ -249,12 +252,17 @@ share/doc/HTML/en/kstars/ekos_astrometry.png
share/doc/HTML/en/kstars/ekos_capture.png
share/doc/HTML/en/kstars/ekos_focus.png
share/doc/HTML/en/kstars/ekos_guide.png
share/doc/HTML/en/kstars/ekos_guide_dithering_settings.png
share/doc/HTML/en/kstars/ekos_guide_gpg_settings.png
share/doc/HTML/en/kstars/ekos_guide_optical_train.png
share/doc/HTML/en/kstars/ekos_guide_phd2.png
share/doc/HTML/en/kstars/ekos_page.png
share/doc/HTML/en/kstars/ekos_profile_guide.png
share/doc/HTML/en/kstars/ekos_profile_guider_select.png
share/doc/HTML/en/kstars/ekos_remote_astrometry.png
share/doc/HTML/en/kstars/ekos_rotator_settings.png
share/doc/HTML/en/kstars/ekos_scheduler.png
share/doc/HTML/en/kstars/ekos_scheduler_settings.png
share/doc/HTML/en/kstars/ekos_summary.png
share/doc/HTML/en/kstars/ekos_summary_cheatsheet.png
share/doc/HTML/en/kstars/ellipticalgalaxies.docbook
@ -282,15 +290,29 @@ share/doc/HTML/en/kstars/flux.docbook
share/doc/HTML/en/kstars/flux.png
share/doc/HTML/en/kstars/flux1.png
share/doc/HTML/en/kstars/flux2.png
share/doc/HTML/en/kstars/focus_adaptive_focus.png
share/doc/HTML/en/kstars/focus_advisor.png
share/doc/HTML/en/kstars/focus_analyze.png
share/doc/HTML/en/kstars/focus_autofocus_log.png
share/doc/HTML/en/kstars/focus_bad_focus.png
share/doc/HTML/en/kstars/focus_ccdfw_group.png
share/doc/HTML/en/kstars/focus_cfz_classic.png
share/doc/HTML/en/kstars/focus_cfz_gold.png
share/doc/HTML/en/kstars/focus_cfz_moustache.png
share/doc/HTML/en/kstars/focus_cfz_wavefront.png
share/doc/HTML/en/kstars/focus_display.png
share/doc/HTML/en/kstars/focus_display_mosaic.png
share/doc/HTML/en/kstars/focus_good_focus.png
share/doc/HTML/en/kstars/focus_mechanics.png
share/doc/HTML/en/kstars/focus_mechanics1.png
share/doc/HTML/en/kstars/focus_process.png
share/doc/HTML/en/kstars/focus_relative_profile.png
share/doc/HTML/en/kstars/focus_settings.png
share/doc/HTML/en/kstars/focus_vcurve.png
share/doc/HTML/en/kstars/focus_vcurve_fourier.png
share/doc/HTML/en/kstars/focus_vcurve_fwhm.png
share/doc/HTML/en/kstars/focus_vcurve_hfradj.png
share/doc/HTML/en/kstars/focus_vcurve_numstars.png
share/doc/HTML/en/kstars/focus_vcurve_timeseries.png
share/doc/HTML/en/kstars/focuser_group.png
share/doc/HTML/en/kstars/fovdialog.png
@ -502,259 +524,6 @@ share/doc/HTML/es/kstars/tools.docbook
share/doc/HTML/es/kstars/utime.docbook
share/doc/HTML/es/kstars/wut.docbook
share/doc/HTML/es/kstars/zenith.docbook
share/doc/HTML/fr/kstars/Add_Object_to_Session_plan.png
share/doc/HTML/fr/kstars/Another_way4.png
share/doc/HTML/fr/kstars/Another_way5.png
share/doc/HTML/fr/kstars/Another_way6.png
share/doc/HTML/fr/kstars/Another_way_to_add.png
share/doc/HTML/fr/kstars/Another_way_to_add_part3.png
share/doc/HTML/fr/kstars/Arp84_EyepieceView.png
share/doc/HTML/fr/kstars/Delete_all_images.png
share/doc/HTML/fr/kstars/EPView_Screenshot.png
share/doc/HTML/fr/kstars/KStars_Neptune.png
share/doc/HTML/fr/kstars/Savin_session.png
share/doc/HTML/fr/kstars/aavso.png
share/doc/HTML/fr/kstars/add-circle.png
share/doc/HTML/fr/kstars/add_object.png
share/doc/HTML/fr/kstars/advanced_page.png
share/doc/HTML/fr/kstars/ai-contents.docbook
share/doc/HTML/fr/kstars/alignment_polaris.png
share/doc/HTML/fr/kstars/alpha.png
share/doc/HTML/fr/kstars/altvstime.docbook
share/doc/HTML/fr/kstars/altvstime.png
share/doc/HTML/fr/kstars/archive-extract.png
share/doc/HTML/fr/kstars/astroinfo.docbook
share/doc/HTML/fr/kstars/astrometry_indexes_settings.png
share/doc/HTML/fr/kstars/astrometry_settings.png
share/doc/HTML/fr/kstars/astrometry_windows_ansvr.png
share/doc/HTML/fr/kstars/blackbody.docbook
share/doc/HTML/fr/kstars/blackbody.png
share/doc/HTML/fr/kstars/calc-angdist.docbook
share/doc/HTML/fr/kstars/calc-angdist.png
share/doc/HTML/fr/kstars/calc-apcoords.docbook
share/doc/HTML/fr/kstars/calc-apcoords.png
share/doc/HTML/fr/kstars/calc-dayduration.docbook
share/doc/HTML/fr/kstars/calc-daylength.png
share/doc/HTML/fr/kstars/calc-ecliptic.docbook
share/doc/HTML/fr/kstars/calc-ecliptic.png
share/doc/HTML/fr/kstars/calc-eqgal.docbook
share/doc/HTML/fr/kstars/calc-eqgal.png
share/doc/HTML/fr/kstars/calc-equinox.docbook
share/doc/HTML/fr/kstars/calc-equinox.png
share/doc/HTML/fr/kstars/calc-geodetic.docbook
share/doc/HTML/fr/kstars/calc-geodetic.png
share/doc/HTML/fr/kstars/calc-horizontal.docbook
share/doc/HTML/fr/kstars/calc-horizontal.png
share/doc/HTML/fr/kstars/calc-julian.png
share/doc/HTML/fr/kstars/calc-julianday.docbook
share/doc/HTML/fr/kstars/calc-planetcoords.docbook
share/doc/HTML/fr/kstars/calc-planetcoords.png
share/doc/HTML/fr/kstars/calc-sidereal.docbook
share/doc/HTML/fr/kstars/calc-sidereal.png
share/doc/HTML/fr/kstars/calculator.docbook
share/doc/HTML/fr/kstars/calibration_settings.png
share/doc/HTML/fr/kstars/capture_settings.png
share/doc/HTML/fr/kstars/catalog_details.png
share/doc/HTML/fr/kstars/center_telescope.png
share/doc/HTML/fr/kstars/cequator.docbook
share/doc/HTML/fr/kstars/color_editor.png
share/doc/HTML/fr/kstars/color_indices.png
share/doc/HTML/fr/kstars/colorandtemp.docbook
share/doc/HTML/fr/kstars/colors_page.png
share/doc/HTML/fr/kstars/commands.docbook
share/doc/HTML/fr/kstars/config.docbook
share/doc/HTML/fr/kstars/cosmicdist.docbook
share/doc/HTML/fr/kstars/cpoles.docbook
share/doc/HTML/fr/kstars/create_catalog.png
share/doc/HTML/fr/kstars/credits.docbook
share/doc/HTML/fr/kstars/csphere.docbook
share/doc/HTML/fr/kstars/csv_import.png
share/doc/HTML/fr/kstars/csv_import_populated.png
share/doc/HTML/fr/kstars/csv_openngc.png
share/doc/HTML/fr/kstars/dark_library.png
share/doc/HTML/fr/kstars/darkmatter.docbook
share/doc/HTML/fr/kstars/detaildialog.png
share/doc/HTML/fr/kstars/details.docbook
share/doc/HTML/fr/kstars/devicemanager.png
share/doc/HTML/fr/kstars/dialog-ok-apply.png
share/doc/HTML/fr/kstars/document-edit.png
share/doc/HTML/fr/kstars/document-open.png
share/doc/HTML/fr/kstars/dome-park.png
share/doc/HTML/fr/kstars/dome-unpark.png
share/doc/HTML/fr/kstars/draw-text.png
share/doc/HTML/fr/kstars/dso_manager.png
share/doc/HTML/fr/kstars/dss.png
share/doc/HTML/fr/kstars/dumpmode.docbook
share/doc/HTML/fr/kstars/ecliptic.docbook
share/doc/HTML/fr/kstars/ekos-align.docbook
share/doc/HTML/fr/kstars/ekos-analyze.docbook
share/doc/HTML/fr/kstars/ekos-capture.docbook
share/doc/HTML/fr/kstars/ekos-focus.docbook
share/doc/HTML/fr/kstars/ekos-guide.docbook
share/doc/HTML/fr/kstars/ekos-logs.docbook
share/doc/HTML/fr/kstars/ekos-profile-editor.docbook
share/doc/HTML/fr/kstars/ekos-profile-wizard.docbook
share/doc/HTML/fr/kstars/ekos-scheduler.docbook
share/doc/HTML/fr/kstars/ekos-setup.docbook
share/doc/HTML/fr/kstars/ekos-tutorials.docbook
share/doc/HTML/fr/kstars/ekos-user-interface.docbook
share/doc/HTML/fr/kstars/ekos.docbook
share/doc/HTML/fr/kstars/ekos_analyze.png
share/doc/HTML/fr/kstars/ekos_astrometry.png
share/doc/HTML/fr/kstars/ekos_capture.png
share/doc/HTML/fr/kstars/ekos_focus.png
share/doc/HTML/fr/kstars/ekos_guide.png
share/doc/HTML/fr/kstars/ekos_guide_phd2.png
share/doc/HTML/fr/kstars/ekos_page.png
share/doc/HTML/fr/kstars/ekos_profile_guider_select.png
share/doc/HTML/fr/kstars/ekos_remote_astrometry.png
share/doc/HTML/fr/kstars/ekos_rotator_settings.png
share/doc/HTML/fr/kstars/ekos_scheduler.png
share/doc/HTML/fr/kstars/ekos_summary.png
share/doc/HTML/fr/kstars/ekos_summary_cheatsheet.png
share/doc/HTML/fr/kstars/ellipticalgalaxies.docbook
share/doc/HTML/fr/kstars/epoch.docbook
share/doc/HTML/fr/kstars/equinox.docbook
share/doc/HTML/fr/kstars/execute_session_nt.png
share/doc/HTML/fr/kstars/execute_session_the_nt.png
share/doc/HTML/fr/kstars/eyepieceview.docbook
share/doc/HTML/fr/kstars/faq.docbook
share/doc/HTML/fr/kstars/file_settings.png
share/doc/HTML/fr/kstars/filter_settings.png
share/doc/HTML/fr/kstars/find.png
share/doc/HTML/fr/kstars/find2.png
share/doc/HTML/fr/kstars/fits_page.png
share/doc/HTML/fr/kstars/fits_settings.png
share/doc/HTML/fr/kstars/fitsviewer.docbook
share/doc/HTML/fr/kstars/fitsviewer.png
share/doc/HTML/fr/kstars/fitsviewer_embedded.png
share/doc/HTML/fr/kstars/fitsviewer_histogram.png
share/doc/HTML/fr/kstars/fitsviewer_selstat.png
share/doc/HTML/fr/kstars/flag-green.png
share/doc/HTML/fr/kstars/flag-red.png
share/doc/HTML/fr/kstars/flux.docbook
share/doc/HTML/fr/kstars/flux.png
share/doc/HTML/fr/kstars/flux1.png
share/doc/HTML/fr/kstars/flux2.png
share/doc/HTML/fr/kstars/focus_bad_focus.png
share/doc/HTML/fr/kstars/focus_ccdfw_group.png
share/doc/HTML/fr/kstars/focus_display.png
share/doc/HTML/fr/kstars/focus_good_focus.png
share/doc/HTML/fr/kstars/focus_mechanics.png
share/doc/HTML/fr/kstars/focus_process.png
share/doc/HTML/fr/kstars/focus_relative_profile.png
share/doc/HTML/fr/kstars/focus_settings.png
share/doc/HTML/fr/kstars/focus_vcurve.png
share/doc/HTML/fr/kstars/focus_vcurve_timeseries.png
share/doc/HTML/fr/kstars/focuser_group.png
share/doc/HTML/fr/kstars/fovdialog.png
share/doc/HTML/fr/kstars/geocoords.docbook
share/doc/HTML/fr/kstars/geolocator.png
share/doc/HTML/fr/kstars/greatcircle.docbook
share/doc/HTML/fr/kstars/guide_calibration_settings.png
share/doc/HTML/fr/kstars/guide_drift_graphics.png
share/doc/HTML/fr/kstars/guide_guide_settings.png
share/doc/HTML/fr/kstars/guides_page.png
share/doc/HTML/fr/kstars/hips.docbook
share/doc/HTML/fr/kstars/horizon.docbook
share/doc/HTML/fr/kstars/hourangle.docbook
share/doc/HTML/fr/kstars/index.cache.bz2
share/doc/HTML/fr/kstars/index.docbook
share/doc/HTML/fr/kstars/indi.docbook
share/doc/HTML/fr/kstars/indi_page.png
share/doc/HTML/fr/kstars/indiclient.png
share/doc/HTML/fr/kstars/indicontrolpanel.png
share/doc/HTML/fr/kstars/install.docbook
share/doc/HTML/fr/kstars/jmoons.docbook
share/doc/HTML/fr/kstars/jmoons.png
share/doc/HTML/fr/kstars/julianday.docbook
share/doc/HTML/fr/kstars/kstars_annotation.png
share/doc/HTML/fr/kstars/kstars_ekos.png
share/doc/HTML/fr/kstars/kstars_fitsviewer.png
share/doc/HTML/fr/kstars/kstars_hips.png
share/doc/HTML/fr/kstars/kstars_horizon.png
share/doc/HTML/fr/kstars/kstars_indi.png
share/doc/HTML/fr/kstars/lambda_ex.png
share/doc/HTML/fr/kstars/lambda_max.png
share/doc/HTML/fr/kstars/leapyear.docbook
share/doc/HTML/fr/kstars/lightcurve.png
share/doc/HTML/fr/kstars/lightcurves.docbook
share/doc/HTML/fr/kstars/limit_settings.png
share/doc/HTML/fr/kstars/list-add.png
share/doc/HTML/fr/kstars/lock-open.png
share/doc/HTML/fr/kstars/luminosity.docbook
share/doc/HTML/fr/kstars/luminosity.png
share/doc/HTML/fr/kstars/luminosity_ex.png
share/doc/HTML/fr/kstars/magnitude.docbook
share/doc/HTML/fr/kstars/media-playback-pause.png
share/doc/HTML/fr/kstars/media-playback-start.png
share/doc/HTML/fr/kstars/media-record.png
share/doc/HTML/fr/kstars/meridian.docbook
share/doc/HTML/fr/kstars/mosaic_adjust_grid.png
share/doc/HTML/fr/kstars/mosaic_close_pole.png
share/doc/HTML/fr/kstars/mosaic_confirm_equipment.png
share/doc/HTML/fr/kstars/mosaic_create_jobs.png
share/doc/HTML/fr/kstars/mosaic_planner.png
share/doc/HTML/fr/kstars/mosaic_select_grid.png
share/doc/HTML/fr/kstars/newfov.png
share/doc/HTML/fr/kstars/object-rotate-right.png
share/doc/HTML/fr/kstars/observinglist.docbook
share/doc/HTML/fr/kstars/observinglist.png
share/doc/HTML/fr/kstars/obsplanner.docbook
share/doc/HTML/fr/kstars/parallax.docbook
share/doc/HTML/fr/kstars/polar_alignment_result.png
share/doc/HTML/fr/kstars/polar_assistant_main.png
share/doc/HTML/fr/kstars/popup.png
share/doc/HTML/fr/kstars/precession.docbook
share/doc/HTML/fr/kstars/process-stop.png
share/doc/HTML/fr/kstars/profile_editor.png
share/doc/HTML/fr/kstars/profile_editor_scripts.png
share/doc/HTML/fr/kstars/profile_wizard_done.png
share/doc/HTML/fr/kstars/profile_wizard_remote.png
share/doc/HTML/fr/kstars/profile_wizard_select.png
share/doc/HTML/fr/kstars/profile_wizard_welcome.png
share/doc/HTML/fr/kstars/quicktour.docbook
share/doc/HTML/fr/kstars/retrograde.docbook
share/doc/HTML/fr/kstars/satellites_page.png
share/doc/HTML/fr/kstars/scheduler_planner.png
share/doc/HTML/fr/kstars/screen1.png
share/doc/HTML/fr/kstars/scriptbuilder.docbook
share/doc/HTML/fr/kstars/scriptbuilder.png
share/doc/HTML/fr/kstars/sds.png
share/doc/HTML/fr/kstars/security-high.png
share/doc/HTML/fr/kstars/security-low.png
share/doc/HTML/fr/kstars/security-medium.png
share/doc/HTML/fr/kstars/sequence_settings.png
share/doc/HTML/fr/kstars/sidereal.docbook
share/doc/HTML/fr/kstars/skycoords.docbook
share/doc/HTML/fr/kstars/skymapdevice.png
share/doc/HTML/fr/kstars/solarsys.docbook
share/doc/HTML/fr/kstars/solarsystem.png
share/doc/HTML/fr/kstars/solarsystem_page.png
share/doc/HTML/fr/kstars/solver_settings.png
share/doc/HTML/fr/kstars/spiralgalaxies.docbook
share/doc/HTML/fr/kstars/star_colors.png
share/doc/HTML/fr/kstars/star_profile_examine_pixels.png
share/doc/HTML/fr/kstars/star_profile_final.png
share/doc/HTML/fr/kstars/star_profile_main.png
share/doc/HTML/fr/kstars/star_profile_toolbar1.png
share/doc/HTML/fr/kstars/star_profile_toolbar2.png
share/doc/HTML/fr/kstars/star_profile_vertical.png
share/doc/HTML/fr/kstars/stars.docbook
share/doc/HTML/fr/kstars/supernovae_page.png
share/doc/HTML/fr/kstars/telescopes.docbook
share/doc/HTML/fr/kstars/terrain_page.png
share/doc/HTML/fr/kstars/timezones.docbook
share/doc/HTML/fr/kstars/tools.docbook
share/doc/HTML/fr/kstars/utime.docbook
share/doc/HTML/fr/kstars/view-filter.png
share/doc/HTML/fr/kstars/view-fullscreen.png
share/doc/HTML/fr/kstars/view-refresh.png
share/doc/HTML/fr/kstars/viewops.png
share/doc/HTML/fr/kstars/wut.docbook
share/doc/HTML/fr/kstars/wut.png
share/doc/HTML/fr/kstars/xplanet_page.png
share/doc/HTML/fr/kstars/zenith.docbook
share/doc/HTML/nl/kstars/aavso.png
share/doc/HTML/nl/kstars/ai-contents.docbook
share/doc/HTML/nl/kstars/altvstime.docbook

4
astro/mepo/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1675222988
SHA256 (mepo-1.1.2.tar.gz) = 5eb1963947be0403452cd1b817a62392cf7d72193f97f7bec096eb72adf8aea3
SIZE (mepo-1.1.2.tar.gz) = 591041
SHA256 (mepo-1.1.2.tar.gz) = d2dd93988fc75964715051720cbc30b6c2b8646812b508fa4e25495fbe33b284
SIZE (mepo-1.1.2.tar.gz) = 590350

3
astro/wcslib/Makefile
View File

@ -1,6 +1,5 @@
PORTNAME= wcslib
PORTVERSION= 7.12
PORTREVISION= 2
PORTVERSION= 8.1
CATEGORIES= astro
MASTER_SITES= ftp://ftp.atnf.csiro.au/pub/software/wcslib/

6
astro/wcslib/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1664110010
SHA256 (wcslib-7.12.tar.bz2) = 9cf8de50e109a97fa04511d4111e8d14bd0a44077132acf73e6cf0029fe96bd4
SIZE (wcslib-7.12.tar.bz2) = 2989693
TIMESTAMP = 1691649266
SHA256 (wcslib-8.1.tar.bz2) = 2bf23e6fabd10b8aecffa54431bf25aa224ff019c60a9e676aa56561f9b4129e
SIZE (wcslib-8.1.tar.bz2) = 3044200

15
astro/wcslib/pkg-plist
View File

@ -56,8 +56,8 @@ include/wcslib-%%VERSION%%/wtbarr.h
lib/libwcs-%%VERSION%%.a
lib/libwcs.a
lib/libwcs.so
lib/libwcs.so.7
lib/libwcs.so.7.12
lib/libwcs.so.8
lib/libwcs.so.8.1
libdata/pkgconfig/wcslib.pc
%%CFITSIO%%man/man1/HPXcvt.1.gz
man/man1/fitshdr.1.gz
@ -73,7 +73,6 @@ man/man1/tofits.1.gz
%%PORTDOCS%%%%DOCSDIR%%/html/annotated.html
%%PORTDOCS%%%%DOCSDIR%%/html/bc_s.png
%%PORTDOCS%%%%DOCSDIR%%/html/bc_sd.png
%%PORTDOCS%%%%DOCSDIR%%/html/bdwn.png
%%PORTDOCS%%%%DOCSDIR%%/html/cel_8h.html
%%PORTDOCS%%%%DOCSDIR%%/html/cel_8h_source.html
%%PORTDOCS%%%%DOCSDIR%%/html/classes.html
@ -83,16 +82,18 @@ man/man1/tofits.1.gz
%%PORTDOCS%%%%DOCSDIR%%/html/dir_af99bb3c152a306abd27951285ad1127.html
%%PORTDOCS%%%%DOCSDIR%%/html/dis_8h.html
%%PORTDOCS%%%%DOCSDIR%%/html/dis_8h_source.html
%%PORTDOCS%%%%DOCSDIR%%/html/doc.png
%%PORTDOCS%%%%DOCSDIR%%/html/docd.png
%%PORTDOCS%%%%DOCSDIR%%/html/doc.svg
%%PORTDOCS%%%%DOCSDIR%%/html/docd.svg
%%PORTDOCS%%%%DOCSDIR%%/html/doxygen.css
%%PORTDOCS%%%%DOCSDIR%%/html/doxygen.svg
%%PORTDOCS%%%%DOCSDIR%%/html/dynsections.js
%%PORTDOCS%%%%DOCSDIR%%/html/files.html
%%PORTDOCS%%%%DOCSDIR%%/html/fitshdr_8h.html
%%PORTDOCS%%%%DOCSDIR%%/html/fitshdr_8h_source.html
%%PORTDOCS%%%%DOCSDIR%%/html/folderclosed.png
%%PORTDOCS%%%%DOCSDIR%%/html/folderopen.png
%%PORTDOCS%%%%DOCSDIR%%/html/folderclosed.svg
%%PORTDOCS%%%%DOCSDIR%%/html/folderclosedd.svg
%%PORTDOCS%%%%DOCSDIR%%/html/folderopen.svg
%%PORTDOCS%%%%DOCSDIR%%/html/folderopend.svg
%%PORTDOCS%%%%DOCSDIR%%/html/form_0.png
%%PORTDOCS%%%%DOCSDIR%%/html/form_1.png
%%PORTDOCS%%%%DOCSDIR%%/html/form_10.png

4
audio/a2jmidid/Makefile
View File

@ -1,6 +1,6 @@
PORTNAME= a2jmidid
PORTVERSION= 9
PORTREVISION= 2
PORTREVISION= 3
CATEGORIES= audio
MAINTAINER= ports@FreeBSD.org
@ -30,7 +30,7 @@ DEBUG_CFLAGS= "-DDEBUG"
.include <bsd.port.options.mk>
.if ${ARCH} == powerpc64 || ${ARCH} == riscv64
.if ${ARCH} == riscv64
MESON_ARGS+= -Db_lto=false
.endif

2
audio/csound/Makefile
View File

@ -1,6 +1,6 @@
PORTNAME= csound
DISTVERSION= 6.15.0
PORTREVISION= 9
PORTREVISION= 10
CATEGORIES= audio lang
MAINTAINER= yuri@FreeBSD.org

12
audio/madronalib/Makefile
View File

@ -2,7 +2,7 @@ PORTNAME= madronalib
DISTVERSIONPREFIX= v
DISTVERSION= 1.6-1016
DISTVERSIONSUFFIX= -g103895f
PORTREVISION= 3
PORTREVISION= 4
CATEGORIES= audio
MAINTAINER= yuri@FreeBSD.org
@ -19,21 +19,19 @@ BROKEN_riscv64= error: use of undeclared identifier '__builtin_ia32_emms'; did y
LIB_DEPENDS= libjack.so:audio/jack
USES= cmake localbase:ldflags perl5
USES= cmake compiler:c++11-lib localbase:ldflags perl5
USE_GITHUB= yes
GH_ACCOUNT= madronalabs
CMAKE_ON= LINUX_JACK
CXXFLAGS_powerpc64le= -DNO_WARN_X86_INTRINSICS
CXXFLAGS_powerpc64= -DNO_WARN_X86_INTRINSICS
.include <bsd.port.options.mk>
.if ${ARCH} == powerpc64
CXXFLAGS+= -DNO_WARN_X86_INTRINSICS -maltivec -mvsx
USES+= compiler:gcc-c++11-lib
.else
USES+= compiler:c++11-lib
.if ${ARCH} == powerpc64 && !defined(CPUTYPE)
CXXFLAGS+= -mcpu=power7
.endif
.include <bsd.port.mk>

6
audio/plasma5-kpipewire/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1688022841
SHA256 (KDE/plasma/5.27.6/kpipewire-5.27.6.tar.xz) = 7ed653bfc0e82aa32e05766def3466937a5b2e31abbf3d50c9298b23e6e4328b
SIZE (KDE/plasma/5.27.6/kpipewire-5.27.6.tar.xz) = 59796
TIMESTAMP = 1691384976
SHA256 (KDE/plasma/5.27.7/kpipewire-5.27.7.tar.xz) = 0ad273b8875c0472e0b4f4332c9f1a5d93dca6533f978fd0606094bd91d24782
SIZE (KDE/plasma/5.27.7/kpipewire-5.27.7.tar.xz) = 59796

1
audio/plasma5-plasma-pa/Makefile
View File

@ -1,6 +1,5 @@
PORTNAME= plasma-pa
DISTVERSION= ${KDE_PLASMA_VERSION}
PORTREVISION= 2
CATEGORIES= audio kde kde-plasma
MAINTAINER= kde@FreeBSD.org

6
audio/plasma5-plasma-pa/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1688022843
SHA256 (KDE/plasma/5.27.6/plasma-pa-5.27.6.tar.xz) = 4e7608ba32a47affe64bb77ec30bc3ed977a4ca7577399238dd3821df5856e4f
SIZE (KDE/plasma/5.27.6/plasma-pa-5.27.6.tar.xz) = 163288
TIMESTAMP = 1691384977
SHA256 (KDE/plasma/5.27.7/plasma-pa-5.27.7.tar.xz) = 4c73fb72af73a5258fb7d384eea65084b76341ae9c55652a491e1163cb46e2ed
SIZE (KDE/plasma/5.27.7/plasma-pa-5.27.7.tar.xz) = 163440

2
audio/polyphone/Makefile
View File

@ -1,6 +1,6 @@
PORTNAME= polyphone
DISTVERSION= 2.3.0
PORTREVISION= 4
PORTREVISION= 5
CATEGORIES= audio
MAINTAINER= yuri@FreeBSD.org

2
audio/sc3-plugins/Makefile
View File

@ -1,7 +1,7 @@
PORTNAME= sc3-plugins
DISTVERSIONPREFIX= Version-
DISTVERSION= 3.9.0
PORTREVISION= 12
PORTREVISION= 13
CATEGORIES= audio
MAINTAINER= yuri@FreeBSD.org

21
audio/stk/Makefile
View File

@ -1,5 +1,5 @@
PORTNAME= stk
PORTVERSION= 4.6.2
DISTVERSION= 5.0.0
PORTREVISION= 1
CATEGORIES= audio
MASTER_SITES= http://ccrma.stanford.edu/software/stk/release/
@ -11,20 +11,31 @@ WWW= https://ccrma.stanford.edu/software/stk
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
LIB_DEPENDS= libjack.so:audio/jack
USES= autoreconf compiler:c++11-lang dos2unix gmake localbase pkgconfig
USES= compiler:c++11-lang dos2unix gmake localbase pkgconfig
USE_LDCONFIG= yes
DOS2UNIX_GLOB= *.cpp *.h
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --with-jack --with-oss
MAKE_ARGS= RAWWAVES=${DATADIR}/rawwaves/
LDFLAGS+= -pthread
OPTIONS_RADIO= BACKEND
OPTIONS_RADIO_BACKEND= JACK OSS
OPTIONS_DEFAULT= JACK
BACKEND_DESC= Audio Backend
JACK_CONFIGURE_WITH= jack
JACK_LIB_DEPENDS= libjack.so:audio/jack
OSS_CONFIGURE_WITH= oss
# OSS option appears to make real-time functionality in STK broken
# (example https://www.music.mcgill.ca/~gary/618/week2/node16.html),
# also see https://github.com/thestk/stk/issues/141#issuecomment-1673488078
post-install:
@cd ${WRKSRC} && ${COPYTREE_SHARE} rawwaves ${STAGEDIR}${DATADIR}
@${RM} ${STAGEDIR}${DATADIR}/rawwaves/._* ${STAGEDIR}${DATADIR}/rawwaves/*.c

6
audio/stk/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1637267004
SHA256 (stk-4.6.2.tar.gz) = 573e26ccf72ce436a1dc4ee3bea05fd35e0a8e742c339c7f5b85225502238083
SIZE (stk-4.6.2.tar.gz) = 2618125
TIMESTAMP = 1691561974
SHA256 (stk-5.0.0.tar.gz) = 0e97d8d2ef0d0d3dd4255fed6d71fcbd832f9977bd1031d2166cdbb865529f11
SIZE (stk-5.0.0.tar.gz) = 2830586

101
audio/stk/files/patch-configure Normal file
View File

@ -0,0 +1,101 @@
--- configure.orig 2023-08-04 15:25:31 UTC
+++ configure
@@ -6220,7 +6220,7 @@ then :
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: using OSS" >&5
printf "%s\n" "using OSS" >&6; }
api="$api -D__LINUX_OSS__"
- LIBS="$LIBS -lossaudio"
+ #LIBS="$LIBS -lossaudio"
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for pthread_create in -lpthread" >&5
printf %s "checking for pthread_create in -lpthread... " >&6; }
if test ${ac_cv_lib_pthread_pthread_create+y}
@@ -6228,7 +6228,7 @@ then :
printf %s "(cached) " >&6
else $as_nop
ac_check_lib_save_LIBS=$LIBS
-LIBS="-lpthread $LIBS"
+LIBS="-pthread $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
@@ -6260,7 +6260,7 @@ if test "x$ac_cv_lib_pthread_pthread_create" = xyes
then :
printf "%s\n" "#define HAVE_LIBPTHREAD 1" >>confdefs.h
- LIBS="-lpthread $LIBS"
+ LIBS="-pthread $LIBS"
else $as_nop
as_fn_error $? "RtAudio requires the pthread library!" "$LINENO" 5
@@ -6276,7 +6276,7 @@ then :
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: using OSS" >&5
printf "%s\n" "using OSS" >&6; }
api="$api -D__LINUX_OSS__"
- LIBS="$LIBS -lossaudio"
+ #LIBS="$LIBS -lossaudio"
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for pthread_create in -lpthread" >&5
printf %s "checking for pthread_create in -lpthread... " >&6; }
if test ${ac_cv_lib_pthread_pthread_create+y}
@@ -6284,7 +6284,7 @@ then :
printf %s "(cached) " >&6
else $as_nop
ac_check_lib_save_LIBS=$LIBS
-LIBS="-lpthread $LIBS"
+LIBS="-pthread $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
@@ -6316,7 +6316,7 @@ if test "x$ac_cv_lib_pthread_pthread_create" = xyes
then :
printf "%s\n" "#define HAVE_LIBPTHREAD 1" >>confdefs.h
- LIBS="-lpthread $LIBS"
+ LIBS="-pthread $LIBS"
else $as_nop
as_fn_error $? "RtAudio requires the pthread library!" "$LINENO" 5
@@ -6325,7 +6325,7 @@ fi
fi
;;
- *-*-linux*)
+ *-*-linux* | *-*-freebsd*)
# Look for ALSA flag
# Check whether --with-alsa was given.
@@ -6617,7 +6617,7 @@ then :
printf %s "(cached) " >&6
else $as_nop
ac_check_lib_save_LIBS=$LIBS
-LIBS="-lpthread $LIBS"
+LIBS="-pthread $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
@@ -6649,7 +6649,7 @@ if test "x$ac_cv_lib_pthread_pthread_create" = xyes
then :
printf "%s\n" "#define HAVE_LIBPTHREAD 1" >>confdefs.h
- LIBS="-lpthread $LIBS"
+ LIBS="-pthread $LIBS"
else $as_nop
as_fn_error $? "RtAudio requires the pthread library!" "$LINENO" 5
@@ -6711,7 +6711,7 @@ then :
printf %s "(cached) " >&6
else $as_nop
ac_check_lib_save_LIBS=$LIBS
-LIBS="-lpthread $LIBS"
+LIBS="-pthread $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
@@ -6743,7 +6743,7 @@ if test "x$ac_cv_lib_pthread_pthread_create" = xyes
then :
printf "%s\n" "#define HAVE_LIBPTHREAD 1" >>confdefs.h
- LIBS="-lpthread $LIBS"
+ LIBS="-pthread $LIBS"
else $as_nop
as_fn_error $? "RtAudio requires the pthread library!" "$LINENO" 5

60
audio/stk/files/patch-configure.ac
View File

@ -1,60 +0,0 @@
--- configure.ac.orig 2021-11-18 02:08:39 UTC
+++ configure.ac
@@ -89,7 +89,6 @@ if test "$debug" = "yes"; then
else
AC_SUBST( debug, [no] )
AC_SUBST( cppflag, [] )
- AC_SUBST( cxxflag, [-O3] )
AC_SUBST( object_path, [Release] )
fi
AC_MSG_RESULT($debug)
@@ -104,7 +103,7 @@ fi
CPPFLAGS="$CPPFLAGS $cppflag"
# For debugging and optimization ... overwrite default because it has both -g and -O2
-CXXFLAGS="$cxxflag"
+CXXFLAGS="$CXXFLAGS $cxxflag"
# Check compiler and use -Wall if gnu.
if [test $GXX = "yes" ;] then
@@ -154,27 +153,27 @@ api="$api -D__UNIX_JACK__"
AC_CHECK_LIB(pthread, pthread_create, , AC_MSG_ERROR(RtAudio requires the pthread library!))])
;;
- *-*-linux*)
+ *-*-linux*|*-*-freebsd*)
# Look for ALSA flag
- AC_ARG_WITH(alsa, [ --with-alsa = choose native ALSA API support (linux only)])
- AS_IF([test "x$with_alsa" == "xyes"], [
- api="$api -D__LINUX_ALSA__"
- AC_MSG_RESULT(using ALSA)
- AC_CHECK_LIB(asound, snd_pcm_open, , AC_MSG_ERROR(ALSA support requires the asound library!))])
+ #AC_ARG_WITH(alsa, [ --with-alsa = choose native ALSA API support (linux only)])
+ #AS_IF([test "x$with_alsa" == "xyes"], [
+ #api="$api -D__LINUX_ALSA__"
+ #AC_MSG_RESULT(using ALSA)
+ #AC_CHECK_LIB(asound, snd_pcm_open, , AC_MSG_ERROR(ALSA support requires the asound library!))])
# Look for OSS flag
AC_ARG_WITH(oss, [ --with-oss = choose OSS API support (unixes only)])
AS_IF([test "x$with_oss" == "xyes"], [
- api="$api -D__LINUX_OSS__ -D__LINUX_ALSA__"
+ api="$api -D__LINUX_OSS__"
AC_MSG_RESULT(using OSS)
- AC_CHECK_LIB(asound, snd_pcm_open, , AC_MSG_ERROR(OSS support requires ALSA for RtMidi!))])
+ #AC_CHECK_LIB(asound, snd_pcm_open, , AC_MSG_ERROR(OSS support requires ALSA for RtMidi!))])
# If no audio api flags specified, use ALSA
- AS_IF([test "$api" == ""], [
- AC_MSG_RESULT(using ALSA)
- AC_SUBST( api, [-D__LINUX_ALSA__] )
- AC_CHECK_LIB(asound, snd_pcm_open, , AC_MSG_ERROR(ALSA support requires the asound library!))
- ])
+ #AS_IF([test "$api" == ""], [
+ # AC_MSG_RESULT(using ALSA)
+ # AC_SUBST( api, [-D__LINUX_ALSA__] )
+ # AC_CHECK_LIB(asound, snd_pcm_open, , AC_MSG_ERROR(ALSA support requires the asound library!))
+ #])
AC_CHECK_LIB(pthread, pthread_create, , AC_MSG_ERROR(RtAudio requires the pthread library!))
;;

2
audio/stk/pkg-plist
View File

@ -102,7 +102,7 @@ include/stk/Whistle.h
include/stk/Wurley.h
include/stk/WvIn.h
include/stk/WvOut.h
lib/libstk-4.6.2.so
lib/libstk-5.0.0.so
lib/libstk.so
%%DATADIR%%/rawwaves/ahh.raw
%%DATADIR%%/rawwaves/bassdrum.raw

8
audio/zrythm/Makefile
View File

@ -1,7 +1,7 @@
PORTNAME= zrythm
DISTVERSIONPREFIX= v
DISTVERSION= 1.0.0-alpha.26.0.13
PORTREVISION= 9
PORTREVISION= 10
CATEGORIES= audio
MAINTAINER= yuri@FreeBSD.org
@ -63,12 +63,6 @@ LDFLAGS+= ${LOCALBASE}/lib/libfftw3_threads.so ${LOCALBASE}/lib/libfftw3f_thread
BINARY_ALIAS= git=false python3=${PYTHON_CMD}
.include <bsd.port.options.mk>
.if ${ARCH} == powerpc64
MESON_ARGS= -Db_lto=false
.endif
post-patch: # https://git.zrythm.org/zrythm/zrythm/issues/299
@${REINPLACE_CMD} 's|<malloc.h>|<stdlib.h>|' ${WRKSRC}/ext/midilib/src/*.c

6
biology/hyphy/Makefile
View File

@ -1,5 +1,5 @@
PORTNAME= hyphy
DISTVERSION= 2.5.51hf
DISTVERSION= 2.5.52
CATEGORIES= biology
MAINTAINER= jrm@FreeBSD.org
@ -9,7 +9,7 @@ WWW= https://www.hyphy.org/
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
ONLY_FOR_ARCHS= aarch64 amd64 armv7 i386 powerpc powerpc64 powerpc64le
ONLY_FOR_ARCHS= aarch64 amd64 i386 powerpc powerpc64 powerpc64le
LIB_DEPENDS= libcurl.so:ftp/curl
TEST_DEPENDS= bash:shells/bash
@ -24,6 +24,4 @@ AVX_DESC= Advanced vector extensions support
AVX_CMAKE_OFF= -DNOAVX:BOOL=ON
# FEL test is failing. See https://github.com/veg/hyphy/issues/1585
.include <bsd.port.mk>

6
biology/hyphy/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1685303680
SHA256 (veg-hyphy-2.5.51hf_GH0.tar.gz) = 403a5d07a4e7e67d3d8136fa83649713ad28223a2519e5fba3aa82697a03375f
SIZE (veg-hyphy-2.5.51hf_GH0.tar.gz) = 5620954
TIMESTAMP = 1691588992
SHA256 (veg-hyphy-2.5.52_GH0.tar.gz) = 9e57d7af4a2bb765c48e4eccd025f22a64b692e8951f258e7b9134f7bd8bffed
SIZE (veg-hyphy-2.5.52_GH0.tar.gz) = 5633837

12
biology/hyphy/files/patch-src_core_include_likefunc.h
View File

@ -1,12 +0,0 @@
--- src/core/include/likefunc.h.orig 2023-06-27 12:50:39 UTC
+++ src/core/include/likefunc.h
@@ -282,9 +282,6 @@ class _LikelihoodFunction: public BaseObj { (public)
long GetThreadCount (void) {
return 1L;
}
- void SetThreadCount (long) {
-
- }
#endif
#endif

1
biology/hyphy/pkg-plist
View File

@ -190,6 +190,7 @@ bin/hyphy
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/contrast-meme.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf

124
biology/sra-tools/Makefile
View File

@ -1,109 +1,67 @@
PORTNAME= sra-tools
DISTVERSION= 2.11.0
PORTREVISION= 4
CATEGORIES= biology
DISTVERSION= 3.0.6
CATEGORIES= biology java
MAINTAINER= jwb@FreeBSD.org
COMMENT= NCBI's toolkit for handling data in INSDC Sequence Read Archives
WWW= https://github.com/ncbi/sra-tools/wiki
WWW= https://github.com/ncbi/sra-tools
LICENSE= PD LGPL21+
LICENSE_COMB= multi
LICENSE_FILE_PD= ${WRKSRC}/LICENSE
LICENSE_DISTFILES_LGPL21+ =
ONLY_FOR_ARCHS= amd64
ONLY_FOR_ARCHS_REASON= NCBI-VDB requires SSE2 instructions, no 32-bit support
# Untested on other platforms, aarch64 support was recently added upstream
ONLY_FOR_ARCHS= aarch64 amd64
ONLY_FOR_ARCHS_REASON= Upstream explicitly supports specific platforms
BUILD_DEPENDS= bash:shells/bash \
${LOCALBASE}/lib/libngs-c++.a:biology/ngs-sdk
BUILD_DEPENDS= bash:shells/bash
LIB_DEPENDS= libxml2.so:textproc/libxml2 \
libhdf5.so:science/hdf5 \
libepoll-shim.so:devel/libepoll-shim
libepoll-shim.so:devel/libepoll-shim \
libzstd.so:archivers/zstd
USES= compiler:c11 gmake localbase:ldflags perl5 shebangfix
USE_PERL5= build
USES= bison cmake shebangfix
USE_GITHUB= yes
USE_LDCONFIG= ${PREFIX}/lib64
USE_JAVA= yes
SHEBANG_GLOB= *.sh *.pl
# Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
JAVA_VERSION= 17+
OPTIONS_DEFINE= EXAMPLES
SHEBANG_GLOB= *.sh
GH_ACCOUNT= ncbi
GH_TUPLE+= ncbi:ngs:${DISTVERSION}:ngs/ngs # ported as biology/ngs-sdk
GH_TUPLE+= ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --with-ngs-sdk-prefix=${LOCALBASE} \
--with-ncbi-vdb-sources=${NCBI_VDB_WRKSRC} \
--with-xml2-prefix=${LOCALBASE} \
--with-hdf5-prefix=${LOCALBASE} \
CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}" \
--with-ncbi-vdb-build=${NCBI_VDB_WRKSRC}/amd64-portbld-freebsd$$(${FREEBSD_RELEASE})
MAKE_ARGS= CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" \
INST_ETCDIR=${STAGEDIR}${PREFIX}/etc
WITH_DEBUG= yes
CMAKE_ARGS+= -DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
NCBI_VDB_WRKSRC= ${WRKSRC}/ncbi-vdb
NCBI_VDB_FILESDIR= ${FILESDIR}
FREEBSD_RELEASE= uname -r | cut -d - -f 1
CFLAGS+= -I${WRKSRC}/interfaces/os/sun
CXXFLAGS+= -I${WRKSRC}/interfaces/os/sun
CONFLICTS_INSTALL= kget
BINARY_ALIAS= gcc=${CC} g++=${CXX}
# for port developers, building with these options may fail
OPTIONS_DEFINE= DEBUG OPTIMIZED_CFLAGS TEST
DEBUG_PREVENTS= OPTIMIZED_CFLAGS
DEBUG_CONFIGURE_WITH= debug
OPTIMIZED_CFLAGS_MAKE_ARGS_OFF= OPT=""
TEST_TEST_TARGET= test
TEST_USES= python
# ncbi-vdb build extras
VDB_CONFIGURE_ARGS= \
--with-xml2-prefix=${LOCALBASE} \
--with-hdf5-prefix=${LOCALBASE} \
--prefix=${PREFIX} \
--build=amd64-portbld-freebsd$$(${FREEBSD_RELEASE}) \
CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}"
VDB_MAKE_ARGS+= -j 1 CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}"
MAKE_ENV+= CPATH="${LOCALBASE}/include/libepoll-shim"
CFLAGS+= -I${WRKSRC}/lib
pre-patch:
@${CP} ${FILESDIR}/Makefile.bsd ${NCBI_VDB_WRKSRC}/build/
@${CP} ${FILESDIR}/ld.bsd.*.sh ${NCBI_VDB_WRKSRC}/build/
@${MKDIR} ${NCBI_VDB_WRKSRC}/interfaces/os/bsd
@${CP} -p ${NCBI_VDB_WRKSRC}/interfaces/os/mac/endian.h \
${NCBI_VDB_WRKSRC}/interfaces/os/bsd/
post-patch:
@${GREP} -q '@@PREFIX@@' ${WRKSRC}/ncbi-vdb/libs/kfg/config.c || (echo "@@PREFIX@@ in file/patch-libs_kfg_config.c is overwritten probably due to using 'make makepatch'"; exit 1)
@${REINPLACE_CMD} -e 's#@@PREFIX@@#"${PREFIX}"#' ${WRKSRC}/ncbi-vdb/libs/kfg/config.c
@${LN} -s ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/x86_64 ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/amd64
post-patch-TEST-on:
@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|' ${WRKSRC}/test/kget/Makefile
post-extract:
@${MKDIR} ${WRKSRC}/ncbi-vdb/interfaces/os/bsd
@${CP} ${FILESDIR}/*.h ${WRKSRC}/ncbi-vdb/interfaces/os/bsd
# cd ${WRKDIR} && ${LN} -s ${WRKSRC}/ncbi-vdb .
pre-configure:
@${CP} ${NCBI_VDB_WRKSRC}/setup/os-arch.prl ${WRKSRC}/setup/os-arch.prl
# same as in biology/ncbi-vdb
@${CP} ${NCBI_VDB_FILESDIR}/Makefile.bsd ${WRKSRC}/build/
@${CP} ${NCBI_VDB_WRKSRC}/build/ld.bsd.*.sh ${WRKSRC}/build/
@${MKDIR} ${WRKSRC}/interfaces/override
@${CP} ${NCBI_VDB_WRKSRC}/interfaces/os/sun/atomic32.h ${WRKSRC}/interfaces/override
@${CP} ${FILESDIR}/byteswap.h ${WRKSRC}/interfaces/override
@cd ${WRKSRC}/ncbi-vdb && ./configure ${VDB_CONFIGURE_ARGS}
@${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/ncbi-vdb/build/COMP
@cd ${WRKSRC}/ncbi-vdb && ${DO_MAKE_BUILD} ${VDB_MAKE_ARGS}
# This follows a static patch. Run "make clean patch" before
# updating the patch.
${REINPLACE_CMD} -e 's|/usr/local/etc/ncbi|${PREFIX}/etc/ncbi|g' \
${WRKSRC}/ncbi-vdb/libs/kfg/config.c
${REINPLACE_CMD} -e 's|/usr/local/bin|${PREFIX}/bin|g' \
${WRKSRC}/tools/external/driver-tool/file-path.posix.cpp
cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make
post-build-TEST-on: do-test
post-stage:
${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.${DISTVERSION}
${MV} ${STAGEDIR}${PREFIX}/share/examples ${STAGEDIR}${PREFIX}/share/examples-sratools
${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
${MV} ${STAGEDIR}${PREFIX}/share/examples-sratools/* ${STAGEDIR}${EXAMPLESDIR}
${RMDIR} ${STAGEDIR}${PREFIX}/share/examples-sratools
${MV} ${STAGEDIR}${PREFIX}/share/examples-java ${STAGEDIR}${EXAMPLESDIR}/java
${MV} ${STAGEDIR}${PREFIX}/share/examples-python ${STAGEDIR}${EXAMPLESDIR}/python
do-install:
cd ${WRKSRC}/amd64-portbld-freebsd*/sra-tools/bsd/clang/*/rel/bin && \
for f in `ls *.${PORTVERSION}`; do \
${INSTALL_PROGRAM} $${f} \
${STAGEDIR}${PREFIX}/bin/`basename $${f%%.${PORTVERSION}}`; \
done
post-stage-EXAMPLES-off:
${RM} -r ${STAGEDIR}${EXAMPLESDIR}
.include <bsd.port.mk>

12
biology/sra-tools/distinfo
View File

@ -1,7 +1,5 @@
TIMESTAMP = 1624382289
SHA256 (ncbi-sra-tools-2.11.0_GH0.tar.gz) = 10ac0a4d1fafc274bc107de811891d3e803d0713a247581dece4448231883810
SIZE (ncbi-sra-tools-2.11.0_GH0.tar.gz) = 8966605
SHA256 (ncbi-ngs-2.11.0_GH0.tar.gz) = 5fde50784760c00b403c2cc42ead15a4e9477697ee439f0a16edb4de3f52dfcc
SIZE (ncbi-ngs-2.11.0_GH0.tar.gz) = 1100365
SHA256 (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa
SIZE (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 22277539
TIMESTAMP = 1691599515
SHA256 (ncbi-sra-tools-3.0.6_GH0.tar.gz) = 9fecfd819ee9beaf8a1d3e4b76a5d49e747bc064525b40416e0730a168986348
SIZE (ncbi-sra-tools-3.0.6_GH0.tar.gz) = 44957431
SHA256 (ncbi-ncbi-vdb-3.0.6_GH0.tar.gz) = 4b6f93336bf8664fdcc151d41ea0793f0b0f88cfcb7c2aa049f162a72f905223
SIZE (ncbi-ncbi-vdb-3.0.6_GH0.tar.gz) = 18972238

72
biology/sra-tools/files/Makefile.bsd
View File

@ -1,72 +0,0 @@
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
# default compiler
ifeq (,$(COMP))
COMP = clang
endif
# handle attempts to set cross-compilation architecture
# note that if your installation is set up for cross compilation,
# you can try to enable it on your own.
ifeq (i386,$(ARCH))
i386:
@ true
x86_64:
@ echo "FreeBSD builds do not support cross-compilation to this architecture"
endif
ifeq (x86_64,$(ARCH))
i386:
@ echo "FreeBSD builds do not support cross-compilation to this architecture"
x86_64:
@ true
endif
.PHONY: i386 x86_64
# library prefix
LPFX = lib
# file extensions
OBJX = o
LOBX = pic.o
LIBX = a
SHLX = so
# compilation defines
DEFINES := -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=bsd$(BITS)
# FreeBSD is a Unix variant; for most cases, linux sources do well
OS_DAD = linux
OS_GDAD = unix
# flex+bison: on Mac, use source-controlled generated .c/.h files
YACC = @ true
LEX = @ true
# build matrix
COMPILERS = CLANG GCC

37
biology/sra-tools/files/byteswap.h
View File

@ -1,40 +1,15 @@
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#ifndef _h_byteswap_
#define _h_byteswap_
#ifndef _freebsd_byteswap_h_
#define _freebsd_byteswap_h_
#include <stdint.h>
#include <sys/endian.h>
/* N.B. Sun's BSWAP seems to be macro-based,
meaning that (x) will be evaluated multiple times */
#define __BYTE_ORDER _BYTE_ORDER
#define __BIG_ENDIAN _BIG_ENDIAN
#define __LITTLE_ENDIAN _LITTLE_ENDIAN
#define bswap_16(x) bswap16 (x)
#define bswap_32(x) bswap32 (x)
#define bswap_64(x) bswap64 (x)
#endif /* _h_byteswap_ */
#endif

2
biology/sra-tools/files/endian.h Normal file
View File

@ -0,0 +1,2 @@
#include <sys/endian.h>

47
biology/sra-tools/files/ld.bsd.clang.sh
View File

@ -1,47 +0,0 @@
#!/usr/local/bin/bash
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
# define linker params
LD_EXPORT_GLOBAL="-Wl,--export-dynamic"
LD_MULTIPLE_DEFS="-Wl,-zmuldefs"
LD_STATIC="-Wl,-Bstatic"
LD_DYNAMIC="-Wl,-Bdynamic"
LD_ALL_SYMBOLS="-Wl,-whole-archive"
LD_REF_SYMBOLS="-Wl,-no-whole-archive"
# build command
DLIB_CMD="$LD -shared"
EXE_CMD="$LD"
# versioned output
if [ "$VERS" = "" ]
then
DLIB_CMD="$DLIB_CMD -o $TARG"
EXE_CMD="$EXE_CMD -o $TARG"
else
set-vers $(echo $VERS | tr '.' ' ')
DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ"
EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS"
fi

158
biology/sra-tools/files/ld.bsd.cmn.sh
View File

@ -1,158 +0,0 @@
#!/usr/local/bin/bash
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
# script name
SELF_NAME="$(basename $0)"
# parameters
LD="$1"
ARCH="$2"
BUILD="$3"
shift 3
SRCDIR="$1"
BINDIR="$2"
OUTDIR="$3"
TARG="$4"
NAME="$5"
DBGAP="$6"
shift 6
VERS="$1"
VERSFILE="$2"
DEPFILE="$3"
shift 3
MODE="$1"
SCMFLAGS="$2"
LDFLAGS="$3"
shift 3
LDIRS="$1"
XDIRS="$2"
shift 2
OBJS="$1"
LIBS="$2"
# decode MODE
STATIC=$(expr $MODE % 2)
MODE=$(expr $MODE / 2)
DYLD=$(expr $MODE % 2)
MODE=$(expr $MODE / 2)
KPROC=$(expr $MODE % 2)
MODE=$(expr $MODE / 2)
THREADS=$(expr $MODE % 2)
MODE=$(expr $MODE / 2)
HAVE_M=$(expr $MODE % 2)
MODE=$(expr $MODE / 2)
HAVE_XML=$(expr $MODE % 2)
# decode SCMFLAGS
CHECKSUM=$(expr $SCMFLAGS % 2)
STATICSYSLIBS=$(expr $SCMFLAGS / 2)
# return parameter for find-lib
LIBPATH=''
# initial command state
CMD=''
LD_STATIC_STATE=0
LD_ALL_STATE=0
# for breaking out version
set-vers ()
{
MAJ=$1
MIN=$2
REL=$3
}
# for locating libraries
find-lib ()
{
_lib="lib$1"
_dirs="$2"
LIBPATH=''
while [ "$_dirs" != "" ]
do
_dir="${_dirs%%:*}"
if [ "$_dir" != "" ]
then
if [ -e "$_dir/$_lib" ]
then
while [ -L "$_dir/$_lib" ]
do
_lib=$(readlink -n "$_dir/$_lib")
done
LIBPATH="$_dir/$_lib"
break;
fi
fi
_dirs="${_dirs#$_dir}"
_dirs="${_dirs#:}"
done
}
# setting state
load-static ()
{
if [ $LD_STATIC_STATE -eq 0 ]
then
CMD="$CMD $LD_STATIC"
LD_STATIC_STATE=1
fi
}
load-dynamic ()
{
if [ $LD_STATIC_STATE -eq 1 ]
then
CMD="$CMD $LD_DYNAMIC"
LD_STATIC_STATE=0
fi
}
load-all-symbols ()
{
if [ $LD_ALL_STATE -eq 0 ]
then
CMD="$CMD $LD_ALL_SYMBOLS"
LD_ALL_STATE=1
fi
}
load-ref-symbols ()
{
if [ $LD_ALL_STATE -eq 1 ]
then
CMD="$CMD $LD_REF_SYMBOLS"
LD_ALL_STATE=0
fi
}

308
biology/sra-tools/files/ld.bsd.dlib.sh
View File

@ -1,308 +0,0 @@
#!/usr/local/bin/bash
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
# ===========================================================================
# input library types, and their handling
#
# normal linkage
# -l : find shared or static
# -s : require static
# -d : require shared
#
# static linkage
# -l : require static
# -s : require static
# -d : ignore
# ===========================================================================
# script name
SELF_NAME="$(basename $0)"
BUILD_DIR="$(dirname $0)"
# parameters and common functions
source "${0%dlib.sh}cmn.sh"
# discover tool chain
case "$LD" in
g*)
source "${0%dlib.sh}gcc.sh"
;;
c*)
source "${0%dlib.sh}clang.sh"
;;
*)
echo "$SELF_NAME: unrecognized ld tool - '$LD'"
exit 5
esac
# DLIB_CMD was started in tool-specific source
CMD="$DLIB_CMD $LDFLAGS"
# tack on object files
CMD="$CMD $OBJS"
# list of static libraries used to create dynamic lib
SLIBS=''
# initial dependency upon Makefile and vers file
DEPS="$SRCDIR/Makefile"
if [ "$LIBS" != "" ]
then
# tack on paths
DIRS="$LDIRS:$XDIRS"
while [ "$DIRS" != "" ]
do
DIR="${DIRS%%:*}"
[ "$DIR" != "" ] && CMD="$CMD -L$DIR"
DIRS="${DIRS#$DIR}"
DIRS="${DIRS#:}"
done
# update LD_LIBRARY_PATH
unset LD_LIBRARY_PATH
export LD_LIBRARY_PATH="$LDIRS:$XDIRS"
# tack on libraries, finding as we go
for LIB in $LIBS
do
# strip off switch
LIBNAME="${LIB#-[lsd]}"
# look at linkage
case "$LIB" in
-ldl|-ddl)
# always load libdl as shared library
load-ref-symbols
load-dynamic
# CMD="$CMD -ldl"
;;
-l*)
# normal or dynamic linkage
FOUND=0
if [ $STATIC -eq 0 ]
then
find-lib $LIBNAME.so $LDIRS
if [ "$LIBPATH" != "" ]
then
# found it
FOUND=1
# load normally
load-ref-symbols
load-dynamic
CMD="$CMD -l$LIBNAME"
fi
fi
# try static only
if [ $FOUND -eq 0 ]
then
find-lib $LIBNAME.a $LDIRS
if [ "$LIBPATH" != "" ]
then
# found it
FOUND=1
# add it to dependencies
DEPS="$DEPS $LIBPATH"
SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a"
# load static
load-static
load-all-symbols
CMD="$CMD -l$LIBNAME"
fi
fi
# not found within our directories
if [ $FOUND -eq 0 ]
then
if [ $STATICSYSLIBS -eq 1 ]
then
case "$LIBNAME" in
z|bz2)
# set load to static
load-static
load-all-symbols
;;
*)
# set load to dynamic
load-ref-symbols
load-dynamic
;;
esac
else
# set load to normal
load-ref-symbols
load-dynamic
fi
CMD="$CMD -l$LIBNAME"
fi
;;
-s*)
# force static load
FOUND=0
find-lib $LIBNAME.a $LDIRS
if [ "$LIBPATH" != "" ]
then
# found it
FOUND=1
# add it to dependencies
DEPS="$DEPS $LIBPATH"
SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a"
# load static
load-static
load-all-symbols
CMD="$CMD -l$LIBNAME"
fi
# not found within our directories
if [ $FOUND -eq 0 ]
then
if [ $STATIC -eq 1 ] || [ $STATICSYSLIBS -eq 1 ]
then
# set load to static
load-static
load-all-symbols
else
case "$LIBNAME" in
z|bz2)
# set load to dynamic
load-ref-symbols
load-dynamic
;;
*)
# set load to static
load-static
load-all-symbols
;;
esac
fi
CMD="$CMD -l$LIBNAME"
fi
;;
-d*)
# only dynamic linkage
FOUND=0
if [ $STATIC -eq 0 ]
then
find-lib $LIBNAME.so $LDIRS
if [ "$LIBPATH" != "" ]
then
# found it
FOUND=1
# load normally
load-ref-symbols
load-dynamic
CMD="$CMD -l$LIBNAME"
fi
fi
# not found within our directories
if [ $FOUND -eq 0 ]
then
# set load to normal
load-ref-symbols
load-dynamic
CMD="$CMD -l$LIBNAME"
fi
;;
esac
done
fi
# put state back to normal
load-ref-symbols
load-dynamic
# add in pthreads
if [ $THREADS -ne 0 ]
then
CMD="$CMD -lpthread"
fi
# add in xml
if [ $HAVE_XML -ne 0 ]
then
CMD="$CMD -lxml2"
fi
# add in math library
if [ $HAVE_M -ne 0 ]
then
CMD="$CMD -lm"
fi
# produce shared library
echo "$CMD"
$CMD || exit $?
# produce dependencies
if [ "$DEPFILE" != "" ]
then
echo "$TARG: $DEPS" > "$DEPFILE"
fi
if [ $CHECKSUM -eq 1 ]
then
SCM_DIR="${BUILD_DIR%/*}/scm"
LOGFILE="$SCM_DIR/scm.log"
MSG=">>>>> scm: calling the collect script from ld.linux.dlib.sh <<<<<<"
#echo "$MSG"
echo "$MSG" >> $LOGFILE
"$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5"
fi

326
biology/sra-tools/files/ld.bsd.exe.sh
View File

@ -1,326 +0,0 @@
#!/usr/local/bin/bash
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
# ===========================================================================
# input library types, and their handling
#
# normal linkage
# -l : find shared or static
# -s : require static
# -d : ignore - will be dynamically loaded
#
# static linkage
# -l : require static
# -s : require static
# -d : require static
# ===========================================================================
# script name
SELF_NAME="$(basename $0)"
BUILD_DIR="$(dirname $0)"
# parameters and common functions
source "${0%exe.sh}cmn.sh"
# discover tool chain
case "$LD" in
g*)
source "${0%exe.sh}gcc.sh"
;;
c*)
source "${0%exe.sh}clang.sh"
;;
*)
echo "$SELF_NAME: unrecognized ld tool - '$LD'"
exit 5
esac
# EXE_CMD was started in tool-specific source
CMD="$EXE_CMD $LDFLAGS"
# if building a static executable against dynamic libraries
# the main application will substitute for name lookup
if [ $STATIC -eq 1 ] && [ $DYLD -eq 1 ]
then
# CMD="$CMD $LD_EXPORT_GLOBAL $LD_MULTIPLE_DEFS"
CMD="$CMD $LD_EXPORT_GLOBAL"
fi
# tack on object files
CMD="$CMD $OBJS"
# list of static libraries used to create executable
SLIBS=''
# initial dependency upon Makefile and vers file
DEPS="$SRCDIR/Makefile $VERSFILE"
if [ "$LIBS" != "" ]
then
# tack on paths
DIRS="$LDIRS:$XDIRS"
while [ "$DIRS" != "" ]
do
DIR="${DIRS%%:*}"
[ "$DIR" != "" ] && CMD="$CMD -L$DIR"
DIRS="${DIRS#$DIR}"
DIRS="${DIRS#:}"
done
# update LD_LIBRARY_PATH
unset LD_LIBRARY_PATH
export LD_LIBRARY_PATH="$LDIRS:$XDIRS"
# tack on libraries, finding as we go
for LIB in $LIBS
do
# strip off switch
LIBNAME="${LIB#-[lsd]}"
# look at linkage
case "$LIB" in
-ldl|-ddl)
# always load libdl as shared library
load-ref-symbols
load-dynamic
# CMD="$CMD -ldl"
;;
-l*)
# normal or dynamic linkage
FOUND=0
if [ $STATIC -eq 0 ]
then
find-lib $LIBNAME.so $LDIRS
if [ "$LIBPATH" != "" ]
then
# found it
FOUND=1
# load dynamic
load-dynamic
CMD="$CMD -l$LIBNAME"
fi
fi
# try static only
if [ $FOUND -eq 0 ]
then
find-lib $LIBNAME.a $LDIRS
if [ "$LIBPATH" != "" ]
then
# found it
FOUND=1
# add it to dependencies
DEPS="$DEPS $LIBPATH"
SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a"
# load static
load-static
[ $STATIC -eq 1 ] && load-all-symbols
CMD="$CMD -l$LIBNAME"
fi
fi
# not found within our directories
if [ $FOUND -eq 0 ]
then
# do not need to load all symbols for external libs
[ $STATIC -eq 1 ] && load-ref-symbols
if [ $STATICSYSLIBS -eq 1 ]
then
case "$LIBNAME" in
z|bz2)
# set load to static
load-static
;;
*)
# set load to dynamic
load-dynamic
;;
esac
else
# set load to normal
load-dynamic
fi
CMD="$CMD -l$LIBNAME"
fi
;;
-s*)
# force static load
FOUND=0
find-lib $LIBNAME.a $LDIRS
if [ "$LIBPATH" != "" ]
then
# found it
FOUND=1
# add it to dependencies
DEPS="$DEPS $LIBPATH"
SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a"
# load static
load-static
[ $STATIC -eq 1 ] && load-all-symbols
CMD="$CMD -l$LIBNAME"
fi
# not found within our directories
if [ $FOUND -eq 0 ]
then
# do not need to load all symbols for external libs
[ $STATIC -eq 1 ] && load-ref-symbols
if [ $STATIC -eq 1 ] || [ $STATICSYSLIBS -eq 1 ]
then
# set load to static
load-static
else
# special case for libs we have in "ext"
# that are sometimes requested as static
case "$LIBNAME" in
z|bz2)
# set load to dynamic
load-dynamic
;;
*)
load-static
;;
esac
fi
CMD="$CMD -l$LIBNAME"
fi
;;
-d*)
FOUND=0
if [ $STATIC -eq 1 ]
then
find-lib $LIBNAME.a $LDIRS
if [ "$LIBPATH" != "" ]
then
# found it
FOUND=1
# add it to dependencies
DEPS="$DEPS $LIBPATH"
SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a"
# load static
load-static
load-all-symbols
CMD="$CMD -l$LIBNAME"
fi
# not found within our directories
if [ $FOUND -eq 0 ]
then
load-static
load-all-symbols
CMD="$CMD -l$LIBNAME"
fi
fi
;;
esac
done
fi
# return to normal
load-ref-symbols
load-dynamic
# add in pthreads
if [ $THREADS -ne 0 ]
then
CMD="$CMD -lpthread"
fi
# add in xml
# Doesn't work since ld.sh uses HAVE_XML=32, passed here as part of MODE
if [ "$HAVE_XML2" = "1" ]
then
CMD="$CMD -lxml2"
fi
# For sra-tools tools/*
CMD="$CMD -lepoll-shim -lxml2 -lbz2 -lz"
# add in math library
if [ $HAVE_M -ne 0 ]
then
CMD="$CMD -lm"
fi
# produce shared library
echo $CMD
$CMD || exit $?
# produce dependencies
if [ "$DEPFILE" != "" ]
then
echo "$TARG: $DEPS" > "$DEPFILE"
fi
if [ $CHECKSUM -eq 1 ]
then
SCM_DIR="${BUILD_DIR%/*}/scm"
LOGFILE="$SCM_DIR/scm.log"
MSG=">>>>> scm: calling the collect script from ld.linux.exe.sh <<<<<<"
#echo "$MSG"
echo "$MSG" >> $LOGFILE
"$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5"
fi

47
biology/sra-tools/files/ld.bsd.gcc.sh
View File

@ -1,47 +0,0 @@
#!/usr/local/bin/bash
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
# define linker params
LD_EXPORT_GLOBAL="-Wl,--export-dynamic"
LD_MULTIPLE_DEFS="-Wl,-zmuldefs"
LD_STATIC="-Wl,-Bstatic"
LD_DYNAMIC="-Wl,-Bdynamic"
LD_ALL_SYMBOLS="-Wl,-whole-archive"
LD_REF_SYMBOLS="-Wl,-no-whole-archive"
# build command
DLIB_CMD="$LD -shared"
EXE_CMD="$LD"
# versioned output
if [ "$VERS" = "" ]
then
DLIB_CMD="$DLIB_CMD -o $TARG"
EXE_CMD="$EXE_CMD -o $TARG"
else
set-vers $(echo $VERS | tr '.' ' ')
DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ"
EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS"
fi

98
biology/sra-tools/files/ld.bsd.ln.sh
View File

@ -1,98 +0,0 @@
#!/usr/local/bin/bash
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
# script name
SELF_NAME="$(basename $0)"
# parameters
TYPE="$1"
OUTDIR="$2"
TARG="$3"
NAME="$4"
DBGAP="$5"
EXT="$6"
VERS="$7"
# find target
TARG=$(basename "$TARG")
# put extension back onto name
NAME="$NAME$DBGAP"
STATIC_NAME="$NAME-static"
if [ "$EXT" != "" ]
then
NAME="$NAME.$EXT"
STATIC_NAME="$STATIC_NAME.$EXT"
fi
# break out version
set-vers ()
{
MAJ=$1
MIN=$2
REL=$3
}
set-vers $(echo $VERS | tr '.' ' ')
cd "$OUTDIR" || exit 5
# create link
create-link ()
{
rm -f "$2"
local CMD="ln -s $1 $2"
echo $CMD
$CMD
}
# test for version in target name
if [ "$TARG" != "$NAME.$MAJ.$MIN.$REL" ]
then
# for simple name, create 2 links
if [ "$TARG" = "$NAME" ]
then
create-link "$NAME.$MAJ.$MIN.$REL" "$NAME.$MAJ"
create-link "$NAME.$MAJ" "$NAME"
# for static libraries, create special link
if [ "$TYPE" = "slib" ]
then
create-link "$NAME" "$STATIC_NAME"
fi
# for name with major version in it
elif [ "$TARG" = "$NAME.$MAJ" ]
then
create-link "$NAME.$MAJ.$MIN.$REL" "$NAME.$MAJ"
# for name with major & minor version in it
elif [ "$TARG" = "$NAME.$MAJ.$MIN" ]
then
create-link "$NAME.$MAJ.$MIN.$REL" "$NAME.$MAJ.$MIN"
fi
fi

146
biology/sra-tools/files/ld.bsd.slib.sh
View File

@ -1,146 +0,0 @@
#!/usr/local/bin/bash
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
# ===========================================================================
# input library types, and their handling
#
# normal or static linkage
# -l : require static
# -s : require static
# -d : ignore
# ===========================================================================
# script name
SELF_NAME="$(basename $0)"
BUILD_DIR="$(dirname $0)"
# parameters and common functions
source "${0%slib.sh}cmn.sh"
# initialize command
CMD="ar -rc"
# function to convert an archive into individual object files
convert-static ()
{
# list members
local path="$1"
local mbrs="$(ar -t $path)"
# unpack archive into temporary directory
mkdir -p ld-tmp
if ! cd ld-tmp
then
echo "$SELF_NAME: failed to cd to ld-tmp"
exit 5
fi
ar -x "$path"
# rename and add to source files list
local m=
for m in $mbrs
do
mv $m $LIBNAME-$m
CMD="$CMD ld-tmp/$LIBNAME-$m"
done
# return to prior location
cd - > /dev/null
}
# versioned output
if [ "$VERS" = "" ]
then
CMD="$CMD $TARG"
else
set-vers $(echo $VERS | tr '.' ' ')
CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS"
fi
# tack on object files
CMD="$CMD $OBJS"
# list of static libraries used to create this lib
SLIBS=''
# initial dependency upon Makefile and vers file
DEPS="$SRCDIR/Makefile"
if [ "$LIBS" != "" ]
then
# tack on libraries, finding as we go
for LIB in $LIBS
do
# strip off switch
LIBNAME="${LIB#-[lsd]}"
# look at linkage
case "$LIB" in
-s*)
# force static load
find-lib $LIBNAME.a $LDIRS
if [ "$LIBPATH" != "" ]
then
# add it to dependencies
DEPS="$DEPS $LIBPATH"
SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a"
# convert to individual object files
convert-static "$LIBPATH" || exit $?
fi
;;
esac
done
fi
# produce static library
echo $CMD
$CMD || exit $?
# remove temporaries
rm -rf ld-tmp
# produce dependencies
if [ "$DEPFILE" != "" ] && [ "$DEPS" != "" ]
then
echo "$TARG: $DEPS" > "$DEPFILE"
fi
if [ $CHECKSUM -eq 1 ]
then
SCM_DIR="${BUILD_DIR%/*}/scm"
LOGFILE="$SCM_DIR/scm.log"
MSG=">>>>> scm: calling the collect script from ld.linux.slib.sh <<<<<<"
#echo "$MSG"
echo "$MSG" >> $LOGFILE
"$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5"
fi

43
biology/sra-tools/files/os-native.h Normal file
View File

@ -0,0 +1,43 @@
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#ifndef _h_os_native_
#define _h_os_native_
#ifndef _h_unix_native_
#include "../unix/unix-native.h"
#endif
#ifdef __cplusplus
extern "C" {
#endif
#ifdef __cplusplus
}
#endif
#endif /* _h_os_native_ */

13
biology/sra-tools/files/patch-CMakeLists.txt Normal file
View File

@ -0,0 +1,13 @@
--- CMakeLists.txt.orig 2023-02-01 20:26:19 UTC
+++ CMakeLists.txt
@@ -54,8 +54,8 @@ set(CMAKE_MODULE_PATH
"${CMAKE_CURRENT_SOURCE_DIR}/build"
)
-set( VDB_BINDIR "${CMAKE_BINARY_DIR}/../ncbi-vdb" CACHE PATH "Location of NCBI VDB build directory" )
-set( VDB_INCDIR "${CMAKE_SOURCE_DIR}/../ncbi-vdb/interfaces" CACHE PATH "Location of NCBI VDB include directory" )
+set( VDB_BINDIR "${CMAKE_BINARY_DIR}/ncbi-vdb" CACHE PATH "Location of NCBI VDB build directory" )
+set( VDB_INCDIR "${CMAKE_SOURCE_DIR}/ncbi-vdb/interfaces" CACHE PATH "Location of NCBI VDB include directory" )
include(CTest)
enable_testing()

56
biology/sra-tools/files/patch-build_env.cmake Normal file
View File

@ -0,0 +1,56 @@
--- build/env.cmake.orig 2023-07-10 16:23:35 UTC
+++ build/env.cmake
@@ -69,11 +69,21 @@ if ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "Darwin" )
set(LIBPFX "lib")
set(SHLX "dylib")
set(STLX "a")
+elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "FreeBSD" )
+ set(OS "bsd")
+ set(LIBPFX "lib")
+ set(SHLX "so")
+ set(STLX "a")
elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "Linux" )
set(OS "linux")
set(LIBPFX "lib")
set(SHLX "so")
set(STLX "a")
+elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "NetBSD" )
+ set(OS "bsd")
+ set(LIBPFX "lib")
+ set(SHLX "so")
+ set(STLX "a")
elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "Windows" )
set(OS "windows")
set(LIBPFX "")
@@ -91,6 +101,8 @@ elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "aarc
set(ARCH "arm64")
elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "x86_64")
set(ARCH "x86_64")
+elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "amd64")
+ set(ARCH "x86_64")
elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "AMD64")
set(ARCH "x86_64")
else()
@@ -98,7 +110,11 @@ else()
endif ()
# create variables based entirely upon OS
-if ( "mac" STREQUAL ${OS} )
+if ( "bsd" STREQUAL ${OS} )
+ add_compile_definitions( BSD UNIX )
+ set( LMCHECK "" )
+ set( EXE "" )
+elseif ( "mac" STREQUAL ${OS} )
add_compile_definitions( MAC BSD UNIX )
set( LMCHECK "" )
set( EXE "" )
@@ -380,6 +396,9 @@ endif()
if ( "mac" STREQUAL ${OS} )
include_directories(${VDB_INTERFACES_DIR}/os/mac)
+ include_directories(${VDB_INTERFACES_DIR}/os/unix)
+elseif( "bsd" STREQUAL ${OS} )
+ include_directories(${VDB_INTERFACES_DIR}/os/bsd)
include_directories(${VDB_INTERFACES_DIR}/os/unix)
elseif( "linux" STREQUAL ${OS} )
include_directories(${VDB_INTERFACES_DIR}/os/linux)

11
biology/sra-tools/files/patch-build_ld.linux.exe.sh
View File

@ -1,11 +0,0 @@
--- build/ld.linux.exe.sh.orig 2021-06-20 16:32:05 UTC
+++ build/ld.linux.exe.sh
@@ -313,6 +313,8 @@ then
fi
fi
+CMD="$CMD -lepoll-thread -lbz2 -lz"
+
# add in math library
if [ $HAVE_M -ne 0 ]
then

30
biology/sra-tools/files/patch-hdf5
View File

@ -1,30 +0,0 @@
--- ncbi-vdb/interfaces/ext/hdf5/H5Opublic.h.orig 2021-03-15 18:16:43 UTC
+++ ncbi-vdb/interfaces/ext/hdf5/H5Opublic.h
@@ -150,8 +150,13 @@ H5_DLL hid_t H5Oopen_by_idx(hid_t loc_id, const char *
H5_index_t idx_type, H5_iter_order_t order, hsize_t n, hid_t lapl_id);
H5_DLL htri_t H5Oexists_by_name(hid_t loc_id, const char *name, hid_t lapl_id);
H5_DLL herr_t H5Oget_info(hid_t loc_id, H5O_info_t *oinfo);
+#if H5_VERSION_GE(1,12,0)
+H5_DLL herr_t H5Oget_info_by_name(hid_t loc_id, const char *name, H5O_info_t *oinfo, unsigned fields,
+ hid_t lapl_id);
+#else
H5_DLL herr_t H5Oget_info_by_name(hid_t loc_id, const char *name, H5O_info_t *oinfo,
hid_t lapl_id);
+#endif
H5_DLL herr_t H5Oget_info_by_idx(hid_t loc_id, const char *group_name,
H5_index_t idx_type, H5_iter_order_t order, hsize_t n, H5O_info_t *oinfo,
hid_t lapl_id);
--- ncbi-vdb/libs/hdf5/hdf5dir.c.orig 2021-03-15 18:16:43 UTC
+++ ncbi-vdb/libs/hdf5/hdf5dir.c
@@ -292,7 +292,11 @@ rc_t CC HDF5DirVisitUpdate ( HDF5Dir *self, bool recur
static uint32_t HDF5DirPathTypeOnBuffer( const HDF5Dir *self, const char *buffer )
{
H5O_info_t obj_info;
+#if H5_VERSION_GE(1,12,0)
+ herr_t h5e = H5Oget_info_by_name( self->hdf5_handle, buffer, &obj_info, H5O_INFO_BASIC, H5P_DEFAULT );
+#else
herr_t h5e = H5Oget_info_by_name( self->hdf5_handle, buffer, &obj_info, H5P_DEFAULT );
+#endif
if ( h5e >= 0 )
{
switch( obj_info.type )

27
biology/sra-tools/files/patch-libs_ascp_CMakeLists.txt Normal file
View File

@ -0,0 +1,27 @@
--- libs/ascp/CMakeLists.txt.orig 2023-07-10 16:23:35 UTC
+++ libs/ascp/CMakeLists.txt
@@ -23,12 +23,17 @@
# ===========================================================================
set ( UNIX_SRC unix/connect.c )
+# FIXME: Add BSD-specific ascp-path.c
+# Aspera can be installed and run with linux compat
+set ( BSD_SRC ${UNIX_SRC} linux/ascp-path.c )
set ( LINUX_SRC ${UNIX_SRC} linux/ascp-path.c )
set ( MAC_SRC ${UNIX_SRC} mac/ascp-path.c )
set ( WIN_SRC win/connect.c win/ascp-path.c )
if ( "windows" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${WIN_SRC} )
+elseif( "bsd" STREQUAL ${OS} )
+ set ( OS_SPECIFIC_SRC ${BSD_SRC} )
elseif( "linux" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
elseif( "mac" STREQUAL ${OS} )
@@ -49,4 +54,4 @@ GenerateStaticLibs(ascp
)
add_compile_definitions( __mod__="libs/ascp" )
-include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} )
\ No newline at end of file
+include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} )

10
biology/sra-tools/files/patch-libs_general-writer_general-writer.cpp Normal file
View File

@ -0,0 +1,10 @@
--- libs/general-writer/general-writer.cpp.orig 2023-05-11 11:57:33 UTC
+++ libs/general-writer/general-writer.cpp
@@ -39,6 +39,7 @@
#include <string.h>
#define PROGRESS_EVENT 0
+#define UNUSED(x) ((void)(x))
namespace ncbi
{

30
biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.clang
View File

@ -1,30 +0,0 @@
--- ncbi-vdb/build/Makefile.clang.orig 2021-03-15 18:16:43 UTC
+++ ncbi-vdb/build/Makefile.clang
@@ -24,23 +24,23 @@
# compilers
-CC = @ $(TOP)/build/cc.sh $(OS) 'clang -c' \
+CC = @ $(TOP)/build/cc.sh $(OS) '$(CCNAME) -c' \
$(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD
-CP = @ $(TOP)/build/cc.sh $(OS) 'clang++ -c' \
+CP = @ $(TOP)/build/cc.sh $(OS) '$(CXXNAME) -c' \
$(CHECKSUM) --objx $(OBJX) -stdlib=libc++ --cflags "$(CPFLAGS)" -MD
# C preprocessor
PP = gcc -E $(CFLAGS)
# linkers
-LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang \
+LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CCNAME) \
--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
LPFLAGS = $(LDFLAGS)
-LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang++ \
+LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CXXNAME) \
--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)

25
biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.env
View File

@ -1,25 +0,0 @@
--- ncbi-vdb/build/Makefile.env.orig 2021-03-15 18:16:43 UTC
+++ ncbi-vdb/build/Makefile.env
@@ -333,6 +333,22 @@ INCDIRS = \
$(addprefix -I,$(XTINC) $(NGSINC)) \
-I.
+# linker paths
+LDPATHS =
+
+ifneq (,$(HDF5_LIBDIR))
+ LDPATHS += -L$(HDF5_LIBDIR)
+endif
+ifneq (,$(XML2_LIBDIR))
+ LDPATHS += -L$(XML2_LIBDIR)
+endif
+ifneq (,$(MAGIC_LIBDIR))
+ LDPATHS += -L$(MAGIC_LIBDIR)
+endif
+ifneq (,$(FUSE_LIBDIR))
+ LDPATHS += -L$(FUSE_LIBDIR)
+endif
+
# defines that describe os & architecture
DLLX ?= $(SHLX)

35
biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.gcc
View File

@ -1,35 +0,0 @@
--- ncbi-vdb/build/Makefile.gcc.orig 2017-07-14 21:55:36 UTC
+++ ncbi-vdb/build/Makefile.gcc
@@ -22,25 +22,27 @@
#
# ===========================================================================
+CCNAME ?= gcc
+CXXNAME ?= g++
# compilers
-CC = @ $(TOP)/build/cc.sh $(OS) 'gcc -c' \
+CC = @ $(TOP)/build/cc.sh $(OS) '$(CCNAME) -c' \
$(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD
-CP = @ $(TOP)/build/cc.sh $(OS) 'g++ -c' \
+CP = @ $(TOP)/build/cc.sh $(OS) '$(CXXNAME) -c' \
$(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD
# C preprocessor
-PP = gcc -E $(CFLAGS)
+PP = $(CCNAME) -E $(CFLAGS)
# linkers
-LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \
+LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CCNAME) \
--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
LPFLAGS = $(LDFLAGS)
-LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \
+LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CXXNAME) \
--build $(BUILD) --ldflags "$(LPFLAGS)" $(STATIC) \
$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)

11
biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.install
View File

@ -1,11 +0,0 @@
--- ncbi-vdb/build/Makefile.install.orig 2021-03-15 18:16:43 UTC
+++ ncbi-vdb/build/Makefile.install
@@ -69,7 +69,7 @@ ifeq (1,$(HAVE_HDF5))
endif
-LIB_TARGET = $(INST_LIBDIR)$(BITS)
+LIB_TARGET = $(INST_LIBDIR)
LIBRARIES_WITH_PREFIX = \
$(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL))

31
biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.shell
View File

@ -1,31 +0,0 @@
--- ncbi-vdb/build/Makefile.shell.orig 2017-07-14 21:55:36 UTC
+++ ncbi-vdb/build/Makefile.shell
@@ -36,6 +36,9 @@ endif
ifeq (Linux, $(UNAME))
HOST_OS = linux
endif
+ifeq (FreeBSD, $(UNAME))
+ HOST_OS = bsd
+endif
ifeq (SunOS, $(UNAME))
HOST_OS = sun
ARCHITECTURES = x86_64 i386
@@ -83,6 +86,9 @@ else
ifeq (x86_64, $(MARCH))
HOST_ARCH = x86_64
endif
+ ifeq (amd64, $(MARCH))
+ HOST_ARCH = x86_64
+ endif
ifeq (i86pc, $(MARCH))
HOST_ARCH = x86_64
ARCHITECTURES = x86_64 i386
@@ -93,7 +99,7 @@ else
endif
endif
-ARCH = $(HOST_ARCH)
+override ARCH = $(HOST_ARCH)
REMOTE_ARCH = $(ARCH)
# pick up dependencies from object directory

47
biology/sra-tools/files/patch-ncbi-vdb_build_env.cmake Normal file
View File

@ -0,0 +1,47 @@
--- ncbi-vdb/build/env.cmake.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/build/env.cmake
@@ -75,9 +75,15 @@ set(CMAKE_CXX_EXTENSIONS OFF)
if ( ${CMAKE_SYSTEM_NAME} STREQUAL "Darwin" )
set(OS "mac")
set(SHLX "dylib")
+elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD" )
+ set(OS "bsd")
+ set(SHLX "so")
elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL "Linux" )
set(OS "linux")
set(SHLX "so")
+elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL "NetBSD" )
+ set(OS "bsd")
+ set(SHLX "so")
elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL "Windows" )
set(OS "windows")
else()
@@ -99,6 +105,8 @@ elseif ( ${_system_processor} STREQUAL "x86_64")
set(ARCH "x86_64")
elseif ( ${_system_processor} STREQUAL "AMD64")
set(ARCH "x86_64")
+elseif ( ${_system_processor} STREQUAL "amd64")
+ set(ARCH "x86_64")
else ()
message ( FATAL_ERROR "unknown architecture " ${_system_processor})
endif ()
@@ -110,6 +118,9 @@ if ( "mac" STREQUAL ${OS} )
set(CMAKE_CXX_ARCHIVE_CREATE "<CMAKE_AR> Scr <TARGET> <LINK_FLAGS> <OBJECTS>")
set(CMAKE_C_ARCHIVE_FINISH "<CMAKE_RANLIB> -no_warning_for_no_symbols -c <TARGET>")
set(CMAKE_CXX_ARCHIVE_FINISH "<CMAKE_RANLIB> -no_warning_for_no_symbols -c <TARGET>")
+elseif( "bsd" STREQUAL ${OS} )
+ add_compile_definitions( BSD UNIX )
+ set( LMCHECK "" )
elseif( "linux" STREQUAL ${OS} )
add_compile_definitions( LINUX UNIX )
set( LMCHECK -lmcheck )
@@ -241,6 +252,9 @@ endif()
if ( "mac" STREQUAL ${OS} )
include_directories(interfaces/os/mac)
+ include_directories(interfaces/os/unix)
+elseif( "bsd" STREQUAL ${OS} )
+ include_directories(interfaces/os/bsd)
include_directories(interfaces/os/unix)
elseif( "linux" STREQUAL ${OS} )
include_directories(interfaces/os/linux)

85
biology/sra-tools/files/patch-ncbi-vdb_interfaces_os_sun_atomic32.h
View File

@ -1,85 +0,0 @@
--- ncbi-vdb/interfaces/os/sun/atomic32.h.orig 2021-03-15 18:16:43 UTC
+++ ncbi-vdb/interfaces/os/sun/atomic32.h
@@ -1,3 +1,66 @@
+#ifndef _h_atomic32_
+#define _h_atomic32_
+
+#include <sys/types.h>
+#include <machine/atomic.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * /usr/src/sys/cddl/compat/opensolaris/sys/atomic.h
+ * BSD license
+ */
+
+#if defined(__i386__) || defined(__amd64__) || defined(__arm__)
+/* No spurious failures from fcmpset. */
+#define STRONG_FCMPSET
+#endif
+
+static inline uint32_t
+atomic_cas_32(volatile uint32_t *target, uint32_t cmp, uint32_t newval)
+{
+#ifdef STRONG_FCMPSET
+ (void) atomic_fcmpset_32(target, &cmp, newval);
+#else
+ uint32_t expected = cmp;
+
+ do {
+ if (atomic_fcmpset_32(target, &cmp, newval))
+ break;
+ } while (cmp == expected);
+#endif
+ return (cmp);
+}
+
+static inline void atomic_inc_32(volatile uint32_t *target)
+{
+ atomic_add_32(target, 1);
+}
+
+static __inline uint32_t atomic_add_32_nv(volatile uint32_t *target, int32_t delta)
+{
+ return (atomic_fetchadd_32(target, delta) + delta);
+}
+
+static __inline uint32_t atomic_inc_32_nv(volatile uint32_t *target)
+{
+ return (atomic_add_32_nv(target, 1));
+}
+
+static __inline void
+atomic_dec_32(volatile uint32_t *target)
+{
+ atomic_subtract_32(target, 1);
+}
+
+static __inline uint32_t
+atomic_dec_32_nv(volatile uint32_t *target)
+{
+ return (atomic_fetchadd_32(target, -1) - 1);
+}
+
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -23,15 +86,6 @@
* ===========================================================================
*
*/
-
-#ifndef _h_atomic32_
-#define _h_atomic32_
-
-#include <sys/atomic.h>
-
-#ifdef __cplusplus
-extern "C" {
-#endif
#ifndef __inline__
#define __inline__ inline

11
biology/sra-tools/files/patch-ncbi-vdb_libs_align_samextract-lib.cpp Normal file
View File

@ -0,0 +1,11 @@
--- ncbi-vdb/libs/align/samextract-lib.cpp.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/align/samextract-lib.cpp
@@ -48,7 +48,7 @@
#include <stdlib.h>
#include <string.h>
-#if LINUX
+#if BSD || LINUX
#include <unistd.h>
#define DFL_THREAD_COUNT ((int)sysconf( _SC_NPROCESSORS_ONLN ) - 1)
#else

12
biology/sra-tools/files/patch-ncbi-vdb_libs_ext_Makefile
View File

@ -1,12 +0,0 @@
--- ncbi-vdb/libs/ext/Makefile.orig 2021-03-15 18:16:43 UTC
+++ ncbi-vdb/libs/ext/Makefile
@@ -32,9 +32,6 @@ include $(TOP)/build/Makefile.shell
# default
#
SUBDIRS = \
- zlib \
- bzip2 \
- magic \
mbedtls
include $(TOP)/build/Makefile.targets

19
biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_CMakeLists.txt Normal file
View File

@ -0,0 +1,19 @@
--- ncbi-vdb/libs/kapp/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/kapp/CMakeLists.txt
@@ -23,12 +23,16 @@
# ===========================================================================
set ( UNIX_SRC unix/args-conv-os.c unix/sysmain.c )
+# Must patch hw.memsize -> hw.usermem
+set ( BSD_SRC ${UNIX_SRC} mac/ram.c )
set ( LINUX_SRC ${UNIX_SRC} linux/ram.c )
set ( MAC_SRC ${UNIX_SRC} mac/ram.c )
set ( WIN_SRC win/args-conv-os.c win/ram.c win/sysmain.c )
if ( "windows" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${WIN_SRC} )
+elseif( "bsd" STREQUAL ${OS} )
+ set ( OS_SPECIFIC_SRC ${BSD_SRC} )
elseif( "linux" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
elseif( "mac" STREQUAL ${OS} )

17
biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_mac_ram.c Normal file
View File

@ -0,0 +1,17 @@
--- ncbi-vdb/libs/kapp/mac/ram.c.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/kapp/mac/ram.c
@@ -46,7 +46,14 @@ rc_t KAppGetTotalRam ( uint64_t * totalRam )
assert ( totalRam != 0 );
+// FIXME: This file should probably be moved to bsd/ram.c
+#if defined(__APPLE__)
ret = sysctlbyname("hw.memsize", totalRam, &len, NULL, 0 );
+#elif defined(__FreeBSD__) || defined(__NetBSD__)
+ ret = sysctlbyname("hw.usermem", totalRam, &len, NULL, 0 );
+#else
+ #error "You need to add a sysctl for this platform."
+#endif
if ( ret < 0 )
{
int status = errno;

25
biology/sra-tools/files/patch-ncbi-vdb_libs_kfc_CMakeLists.txt Normal file
View File

@ -0,0 +1,25 @@
--- ncbi-vdb/libs/kfc/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/kfc/CMakeLists.txt
@@ -23,12 +23,15 @@
# ===========================================================================
set ( UNIX_SRC unix/sysctx.c unix/sysrsrc.c )
+set ( BSD_SRC ${UNIX_SRC} )
set ( LINUX_SRC ${UNIX_SRC} )
set ( MAC_SRC ${UNIX_SRC} )
set ( WIN_SRC win/sysctx.c win/sysrsrc.c )
if ( "windows" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${WIN_SRC} )
+elseif( "bsd" STREQUAL ${OS} )
+ set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
elseif( "linux" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
elseif( "mac" STREQUAL ${OS} )
@@ -48,4 +51,4 @@ set( SRC
GenerateStaticLibs( kfc "${SRC}" )
add_compile_definitions (__mod__="libs/kfc")
-include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} )
\ No newline at end of file
+include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} )

33
biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_config.c
View File

@ -1,20 +1,31 @@
--- ncbi-vdb/libs/kfg/config.c.orig 2021-03-15 18:16:43 UTC
--- ncbi-vdb/libs/kfg/config.c.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/kfg/config.c
@@ -2577,7 +2577,7 @@ bool load_from_std_location ( KConfig *self, const KDi
@@ -2574,7 +2574,7 @@ bool load_from_std_location ( KConfig *self, const KDi
const char * std_locs [] =
{
#if ! WINDOWS
- "/etc/ncbi",
+ @@PREFIX@@ "/etc/ncbi",
+ "/usr/local/etc/ncbi",
#else
"/c/ncbi",
#endif
@@ -2850,6 +2850,8 @@ void add_predefined_nodes ( KConfig * self, const char
#define OS "win"
#elif SUN
#define OS "sun"
+#elif BSD
@@ -2588,7 +2588,7 @@ bool load_from_std_location ( KConfig *self, const KDi
NCBI_VDB_NO_ETC_NCBI_KFG[0] != '\0')
{
DBGMSG(DBG_KFG, DBG_FLAG(DBG_KFG),
- ("KFG: load from std. location /etc/ncbi is disabled. "
+ ("KFG: load from std. location /usr/local/etc/ncbi is disabled. "
"NCBI_VDB_NO_ETC_NCBI_KFG='%s'\n", NCBI_VDB_NO_ETC_NCBI_KFG));
return loaded;
}
@@ -2839,7 +2839,9 @@ void add_predefined_nodes ( KConfig * self, const char
update_node ( self, "kfg/arch/bits", buf, true );
/* *OS */
-#if LINUX
+#if BSD
+ #define OS "bsd"
#else
#error unrecognized OS
#endif
+#elif LINUX
#define OS "linux"
#elif MAC
#define OS "mac"

35
biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_CMakeLists.txt Normal file
View File

@ -0,0 +1,35 @@
--- ncbi-vdb/libs/kfs/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/kfs/CMakeLists.txt
@@ -23,6 +23,7 @@
# ===========================================================================
set ( UNIX_SRC unix/sysdir.c unix/sysdll.c unix/sysfile.c unix/syslockfile.c unix/sysmmap.c )
+set ( BSD_SRC ${UNIX_SRC} )
set ( LINUX_SRC ${UNIX_SRC} )
set ( MAC_SRC ${UNIX_SRC} )
set ( WIN_SRC win/directory-path.c win/sysdir.c win/sysdll.c win/sysfile.c win/syslockfile.c win/sysmmap.c
@@ -30,6 +31,7 @@ set ( WIN_SRC win/directory-path.c win/sysdir.c win/sy
)
set ( UNIX_SRC_V2 unix/sysfile-v2.c )
+set ( BSD_SRC_V2 ${UNIX_SRC_V2} )
set ( LINUX_SRC_V2 ${UNIX_SRC_V2} )
set ( MAC_SRC_V2 ${UNIX_SRC_V2} )
set ( WIN_SRC_V2 win/sysfile-v2.c )
@@ -37,6 +39,9 @@ set ( WIN_SRC_V2 win/sysfile-v2.c )
if ( "windows" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${WIN_SRC} )
include_directories( win )
+elseif( "bsd" STREQUAL ${OS} )
+ set ( OS_SPECIFIC_SRC ${BSD_SRC} )
+ include_directories( unix )
elseif( "linux" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
include_directories( unix )
@@ -106,4 +111,4 @@ GenerateStaticLibsWithDefs( kfs-nommap ${KFS_NOMMAP_SR
GenerateStaticLibs( kfs "${KFS_SRC}" )
add_compile_definitions (__mod__="libs/kfs")
-include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} )
\ No newline at end of file
+include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} )

11
biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_unix_sysdir.c Normal file
View File

@ -0,0 +1,11 @@
--- ncbi-vdb/libs/kfs/unix/sysdir.c.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/kfs/unix/sysdir.c
@@ -2291,6 +2291,8 @@ rc_t KSysDirOpenDirRead_v1 ( const KSysDir_v1 * self,
rc_t rc;
rc = KSysDirMakePath_v1 ( self, rcOpening, true, full, sizeof full, path, args );
+ // FIXME: Remove this debug statement
+ // fprintf(stderr, "path = %s full = %s\n", path, full);
if ( rc == 0 )
{
int t;

18
biology/sra-tools/files/patch-ncbi-vdb_libs_klib_CMakeLists.txt Normal file
View File

@ -0,0 +1,18 @@
--- ncbi-vdb/libs/klib/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/klib/CMakeLists.txt
@@ -24,12 +24,15 @@
set ( UNIX_BASE_SRC unix/misc.c unix/syslog.c unix/systime.c unix/syswriter.c )
set ( UNIX_SRC ${UNIX_BASE_SRC} unix/syserrcode.c )
+set ( BSD_SRC ${UNIX_SRC} )
set ( LINUX_SRC ${UNIX_BASE_SRC} linux/syserrcode.c )
set ( MAC_SRC ${UNIX_SRC} )
set ( WIN_SRC win/misc.c win/sysalloc.c win/syserrcode.c win/syslog.c win/systime.c win/syswriter.c )
if ( "windows" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${WIN_SRC} )
+elseif( "bsd" STREQUAL ${OS} )
+ set ( OS_SPECIFIC_SRC ${BSD_SRC} )
elseif( "linux" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
elseif( "mac" STREQUAL ${OS} )

20
biology/sra-tools/files/patch-ncbi-vdb_libs_klib_hashfile.c Normal file
View File

@ -0,0 +1,20 @@
--- ncbi-vdb/libs/klib/hashfile.c.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/klib/hashfile.c
@@ -35,7 +35,7 @@
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#if LINUX
+#if BSD || LINUX
#include <sys/mman.h>
#endif
@@ -346,7 +346,7 @@ static void * map_calloc( KHashFile * self, size_t siz
KLockUnlock( self->alloc_lock );
return NULL;
}
-#if LINUX
+#if BSD || LINUX
/* Not sure this helps */
madvise( (void *)self->alloc_base, req, MADV_RANDOM );
#endif

13
biology/sra-tools/files/patch-ncbi-vdb_libs_klib_unix_systime.c
View File

@ -1,11 +1,16 @@
--- ncbi-vdb/libs/klib/unix/systime.c.orig 2017-07-14 21:55:36 UTC
--- ncbi-vdb/libs/klib/unix/systime.c.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/klib/unix/systime.c
@@ -142,7 +142,7 @@ LIB_EXPORT KTime_t CC KTimeMakeTime ( co
@@ -142,7 +142,13 @@ LIB_EXPORT KTime_t CC KTimeMakeTime ( const KTime *sel
t . tm_isdst = self -> dst;
ts = mktime ( &t );
- ts -= timezone;
+ ts += localtime(&ts)->tm_gmtoff;
+#ifdef __FreeBSD__
+ // This might be portable to all platforms
+ ts += localtime(&ts)->tm_gmtoff;
+#else
+ // extern global in sys/time.h on Linux and some other platforms
ts -= timezone;
+#endif
}
return ts;

20
biology/sra-tools/files/patch-ncbi-vdb_libs_kns_CMakeLists.txt Normal file
View File

@ -0,0 +1,20 @@
--- ncbi-vdb/libs/kns/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/kns/CMakeLists.txt
@@ -23,6 +23,7 @@
# ===========================================================================
set ( UNIX_SRC unix/sysmgr.c unix/syssock.c unix/sysstream.c )
+set ( BSD_SRC ${UNIX_SRC} mac/sysendpoint.c mac/syspoll.c )
set ( LINUX_SRC ${UNIX_SRC} linux/sysendpoint.c linux/syspoll.c )
set ( MAC_SRC ${UNIX_SRC} mac/sysendpoint.c mac/syspoll.c )
set ( WIN_SRC win/sysendpoint.c win/sysmgr.c win/syssock.c win/sysstream.c )
@@ -30,6 +31,9 @@ set ( WIN_SRC win/sysendpoint.c win/sysmgr.c win/sysso
if ( "windows" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${WIN_SRC} )
include_directories( win )
+elseif( "bsd" STREQUAL ${OS} )
+ set ( OS_SPECIFIC_SRC ${BSD_SRC} )
+ include_directories( unix )
elseif( "linux" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
include_directories( unix )

11
biology/sra-tools/files/patch-ncbi-vdb_libs_kns_manager.c Normal file
View File

@ -0,0 +1,11 @@
--- ncbi-vdb/libs/kns/manager.c.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/kns/manager.c
@@ -58,7 +58,7 @@
#if HAVE_GNU_LIBC_VERSION_H
#include <gnu/libc-version.h>
#endif
-#if LINUX
+#if BSD || LINUX
#include <arpa/inet.h>
#include <netinet/in.h>
#endif

2
biology/sra-tools/files/patch-ncbi-vdb_libs_kns_unix_syssock.c
View File

@ -1,4 +1,4 @@
--- ncbi-vdb/libs/kns/unix/syssock.c.orig 2017-07-14 21:55:36 UTC
--- ncbi-vdb/libs/kns/unix/syssock.c.orig 2023-08-07 20:34:54 UTC
+++ ncbi-vdb/libs/kns/unix/syssock.c
@@ -66,6 +66,7 @@
#include <sys/types.h>

21
biology/sra-tools/files/patch-ncbi-vdb_libs_kproc_CMakeLists.txt Normal file
View File

@ -0,0 +1,21 @@
--- ncbi-vdb/libs/kproc/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/kproc/CMakeLists.txt
@@ -23,6 +23,7 @@
# ===========================================================================
set ( UNIX_SRC unix/syscond.c unix/systhread.c unix/systimeout.c )
+set ( BSD_SRC ${UNIX_SRC} bsd/syslock.c bsd/sysmgr.c)
set ( LINUX_SRC ${UNIX_SRC} linux/sysbarrier.c linux/syslock.c linux/sysmgr.c )
set ( MAC_SRC ${UNIX_SRC} bsd/syslock.c bsd/sysmgr.c)
set ( WIN_SRC win/syscond.c win/syslock.c win/sysmgr.c win/systhread.c win/systimeout.c )
@@ -30,6 +31,10 @@ set ( WIN_SRC win/syscond.c win/syslock.c win/sysmgr.c
if ( "windows" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${WIN_SRC} )
include_directories( win )
+elseif( "bsd" STREQUAL ${OS} )
+ set ( OS_SPECIFIC_SRC ${BSD_SRC} )
+ include_directories( bsd )
+ include_directories( unix )
elseif( "linux" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
include_directories( linux )

18
biology/sra-tools/files/patch-ncbi-vdb_libs_ktst_CMakeLists.txt Normal file
View File

@ -0,0 +1,18 @@
--- ncbi-vdb/libs/ktst/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/ktst/CMakeLists.txt
@@ -23,12 +23,15 @@
# ===========================================================================
set ( UNIX_SRC unix/systestenv )
+set ( BSD_SRC ${UNIX_SRC} )
set ( LINUX_SRC ${UNIX_SRC} )
set ( MAC_SRC ${UNIX_SRC} )
set ( WIN_SRC win/systestenv )
if ( "windows" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${WIN_SRC} )
+elseif( "bsd" STREQUAL ${OS} )
+ set ( OS_SPECIFIC_SRC ${BSD_SRC} )
elseif( "linux" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
elseif( "mac" STREQUAL ${OS} )

20
biology/sra-tools/files/patch-ncbi-vdb_libs_ncbi-vdb_Makefile
View File

@ -1,20 +0,0 @@
--- ncbi-vdb/libs/ncbi-vdb/Makefile.orig 2021-06-20 15:15:25 UTC
+++ ncbi-vdb/libs/ncbi-vdb/Makefile
@@ -138,9 +138,7 @@ VDB_LIB_CMN = \
klib \
kproc \
$(LIBKQ) \
- kfc \
- bz2 \
- z \
+ kfc
VDB_LIB_RD = \
align-reader \
@@ -198,4 +196,4 @@ fuzz:
$(TOP)/build/ld.sh linux x86_64 gcc --build dbg --ldflags "-g -m64" --objx o --shlx so --libx a --srcdir $(SRCDIR) --bindir $(BINDIR) --slib -o $(FLIBDIR)/libncbi-vdb.$(LIBX) -L$(FLIBDIR) $(VDB_LIB) $(VDB_NGS_LIB)
cleanfuzz:
- rm -rf $(FLIBDIR)/*
\ No newline at end of file
+ rm -rf $(FLIBDIR)/*

12
biology/sra-tools/files/patch-ncbi-vdb_libs_search_Makefile
View File

@ -1,12 +0,0 @@
--- ncbi-vdb/libs/search/Makefile.orig 2017-07-14 21:55:36 UTC
+++ ncbi-vdb/libs/search/Makefile
@@ -39,6 +39,9 @@ OBJFILES = \
include $(TOP)/build/Makefile.env
+CARCH += -msse2
+# nucstrstr.c requires SSE2
+
#-------------------------------------------------------------------------------
# outer targets
#

25
biology/sra-tools/files/patch-ncbi-vdb_libs_vfs_CMakeLists.txt Normal file
View File

@ -0,0 +1,25 @@
--- ncbi-vdb/libs/vfs/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/libs/vfs/CMakeLists.txt
@@ -23,12 +23,15 @@
# ===========================================================================
set ( UNIX_SRC unix/syskeyring.c unix/syspath.c )
+set ( BSD_SRC ${UNIX_SRC} )
set ( LINUX_SRC ${UNIX_SRC} )
set ( MAC_SRC ${UNIX_SRC} )
set ( WIN_SRC win/syskeyring.c win/syspath.c )
if ( "windows" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${WIN_SRC} )
+elseif( "bsd" STREQUAL ${OS} )
+ set ( OS_SPECIFIC_SRC ${BSD_SRC} )
elseif( "linux" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
elseif( "mac" STREQUAL ${OS} )
@@ -54,4 +57,4 @@ set( SRC
GenerateStaticLibs( vfs "${SRC}" )
add_compile_definitions (__mod__="libs/vfs")
-include_directories(${CMAKE_CURRENT_SOURCE_DIR})
\ No newline at end of file
+include_directories(${CMAKE_CURRENT_SOURCE_DIR})

243
biology/sra-tools/files/patch-ncbi-vdb_setup_konfigure.perl
View File

@ -1,243 +0,0 @@
--- ncbi-vdb/setup/konfigure.perl.orig 2021-03-15 18:16:43 UTC
+++ ncbi-vdb/setup/konfigure.perl
@@ -192,7 +192,7 @@ if ($OPT{'help'}) {
foreach (@ARGV) {
@_ = split('=');
next if ($#_ != 1);
- $OPT{$_[0]} = $_[1] if ($_[0] eq 'CXX' || $_[0] eq 'LDFLAGS');
+ $OPT{$_[0]} = $_[1] if ($_[0] eq 'CC' || $_[0] eq 'CXX' || $_[0] eq 'LDFLAGS' || $_[0] eq 'TOOLS');
}
println "Configuring $PACKAGE_NAME package";
@@ -204,7 +204,7 @@ print "checking system type... " unless ($AUTORUN);
my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
println $OSTYPE unless ($AUTORUN);
-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
+unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /freebsd/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
println "configure: error: unsupported system '$OSTYPE'";
exit 1;
}
@@ -225,7 +225,7 @@ if ($OS eq 'linux') {
print "checking machine architecture... " unless ($AUTORUN);
println $MARCH unless ($AUTORUN);
-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) {
+unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) {
println "configure: error: unsupported architecture '$OSTYPE':'$MARCH'";
exit 1;
}
@@ -310,7 +310,7 @@ print "checking for supported architecture... " unless
my $BITS;
-if ($MARCH =~ /x86_64/i) {
+if ($MARCH =~ /(x86_|amd)64/i) {
$BITS = 64;
} elsif ($MARCH eq 'fat86') {
$BITS = '32_64';
@@ -337,6 +337,19 @@ if ($OSTYPE =~ /linux/i) {
$OSINC = 'unix';
$TOOLS = 'gcc' unless ($TOOLS);
$PYTHON = 'python';
+} elsif ($OSTYPE =~ /freebsd/i) {
+ $LPFX = 'lib';
+ $OBJX = 'o';
+ $LOBX = 'pic.o';
+ $LIBX = 'a';
+ $SHLX = 'so';
+ $EXEX = '';
+ $OSINC = 'unix';
+ unless ($TOOLS) {
+ $TOOLS = 'clang';
+ $TOOLS = $OPT{TOOLS} if ($OPT{TOOLS});
+ }
+ $PYTHON = $ENV{FREEBSD_PYTHON_CMD};
} elsif ($OSTYPE =~ /darwin/i) {
$LPFX = 'lib';
$OBJX = 'o';
@@ -362,17 +375,19 @@ my ($ARCH_FL, $DBG, $OPT, $PIC, $INC, $MD, $LDFLAGS) =
print "checking for supported tool chain... " unless ($AUTORUN);
+$CC = $OPT{CC } if ($OPT{CC });
$CPP = $OPT{CXX } if ($OPT{CXX });
$LDFLAGS = $OPT{LDFLAGS} if ($OPT{LDFLAGS});
if ($TOOLS =~ /gcc$/) {
$CPP = 'g++' unless ($CPP);
- $CC = "$TOOLS -c";
+ $CC = 'gcc' unless ($CC);
+ $LD = $CC;
+ $CC = "$CC -c";
$CP = "$CPP -c";
$AR = 'ar rc';
$ARX = 'ar x';
$ARLS = 'ar t';
- $LD = $TOOLS;
$LP = $CPP;
$DBG = '-g -DDEBUG';
@@ -382,21 +397,24 @@ if ($TOOLS =~ /gcc$/) {
$MD = '-MD';
} elsif ($TOOLS eq 'clang') {
$CPP = 'clang++' unless ($CPP);
- $CC = 'clang -c';
- my $versionMin = '-mmacosx-version-min=10.10';
+ $CC = 'clang' unless ($CC);
+ $LD = $CC;
+ $CC = "$CC -c";
+ my $versionMin = '';
+ $versionMin = '-mmacosx-version-min=10.6' if ($OSTYPE =~ /darwin/i);
$CP = "$CPP -c $versionMin";
if ($BITS ne '32_64') {
$ARCH_FL = '-arch i386' if ($BITS == 32);
$OPT = '-O3';
$AR = 'ar rc';
- $LD = "clang $ARCH_FL";
+ $LD = "$LD $ARCH_FL";
$LP = "$CPP $versionMin $ARCH_FL";
} else {
$MAKE_MANIFEST = '( echo "$^" > $@/manifest )';
$ARCH_FL = '-arch i386 -arch x86_64';
$OPT = '-O3';
$AR = 'libtool -static -o';
- $LD = "clang -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
+ $LD = "$LD -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
$LP = "$CPP $versionMin -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
}
$ARX = 'ar x';
@@ -826,13 +844,13 @@ OS_ARCH = \$(shell perl \$(TOP)/setup/os-arch.perl)
# install paths
EndText
- L($F, "INST_BINDIR = $OPT{'bindir'}" ) if ($OPT{'bindir'});
- L($F, "INST_LIBDIR = $OPT{'libdir'}" ) if ($OPT{'libdir'});
- L($F, "INST_INCDIR = $OPT{'includedir'}" ) if ($OPT{'includedir'});
- L($F, "INST_SCHEMADIR = $OPT{'shemadir'}" ) if ($OPT{'shemadir'});
- L($F, "INST_SHAREDIR = $OPT{'sharedir'}" ) if ($OPT{'sharedir'});
- L($F, "INST_JARDIR = $OPT{'javadir'}" ) if ($OPT{'javadir'});
- L($F, "INST_PYTHONDIR = $OPT{'pythondir'}") if ($OPT{'pythondir'});
+ L($F, "INST_BINDIR = \$(DESTDIR)$OPT{'bindir'}" ) if ($OPT{'bindir'});
+ L($F, "INST_LIBDIR = \$(DESTDIR)$OPT{'libdir'}" ) if ($OPT{'libdir'});
+ L($F, "INST_INCDIR = \$(DESTDIR)$OPT{'includedir'}" ) if ($OPT{'includedir'});
+ L($F, "INST_SCHEMADIR = \$(DESTDIR)$OPT{'shemadir'}" ) if ($OPT{'shemadir'});
+ L($F, "INST_SHAREDIR = \$(DESTDIR)$OPT{'sharedir'}" ) if ($OPT{'sharedir'});
+ L($F, "INST_JARDIR = \$(DESTDIR)$OPT{'javadir'}" ) if ($OPT{'javadir'});
+ L($F, "INST_PYTHONDIR = \$(DESTDIR)$OPT{'pythondir'}") if ($OPT{'pythondir'});
my ($E_VERSION_SHLX, $VERSION_SHLX,
$E_MAJVERS_SHLX , $MAJMIN_SHLX, $MAJVERS_SHLX);
@@ -896,7 +914,7 @@ MAJMIN_EXEX = \$(EXEX).\$(MAJMIN)
MAJVERS_EXEX = \$(EXEX).\$(MAJVERS)
# system architecture and wordsize
-ARCH = $ARCH
+override ARCH = $ARCH
EndText
L($F, "# ARCH = $ARCH ( $MARCH )") if ($ARCH ne $MARCH);
@@ -932,7 +950,7 @@ EndText
}
L($F, "PIC = $PIC") if ($PIC);
if ($PKG{LNG} eq 'C') {
- if ($TOOLS =~ /clang/i) {
+ if ($OSTYPE =~ /darwin/i) {
L($F, 'SONAME = -install_name ' .
'$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
L($F, ' -compatibility_version $(MAJMIN) -current_version $(VERSION) \\');
@@ -1043,7 +1061,7 @@ EndText
L($F, '# directory rules');
if ($PKG{LNG} eq 'C') {
L($F, '$(BINDIR) $(LIBDIR) $(ILIBDIR) '
- . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):');
+ . '$(OBJDIR) $(INST_LIBDIR):');
T($F, 'mkdir -p $@');
} elsif ($PKG{LNG} eq 'JAVA') {
# test if we have jni header path
@@ -1073,12 +1091,12 @@ EndText
L($F, 'export CONFIGURE_FOUND_XML2');
L($F);
- if ($OS eq 'linux' || $OS eq 'mac') {
+ if ($OS eq 'linux' || $OS eq 'bsd' || $OS eq 'mac') {
L($F, '# installation rules');
L($F,
- '$(INST_LIBDIR)$(BITS)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
+ '$(INST_LIBDIR)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
T($F, '@ echo -n "installing \'$(@F)\'... "');
- T($F, '@ if cp $^ $@ && chmod 644 $@; \\');
+ T($F, '@ if $(BSD_INSTALL_DATA) $^ $@; \\');
T($F, ' then \\');
T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
. '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@) '
@@ -1087,7 +1105,7 @@ EndText
T($F, ' ln -s $(patsubst %$(VERSION),%$(MAJVERS),$(@F)) '
. '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@); \\');
T($F, ' ln -s $(patsubst %$(VERSION_LIBX),%$(LIBX),$(@F)) ' .
- '$(INST_LIBDIR)$(BITS)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
+ '$(INST_LIBDIR)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
. ' \\');
T($F, ' echo success; \\');
T($F, ' else \\');
@@ -1097,15 +1115,15 @@ EndText
L($F);
L($F,
- '$(INST_LIBDIR)$(BITS)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
+ '$(INST_LIBDIR)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
T($F, '@ echo -n "installing \'$(@F)\'... "');
- T($F, '@ if cp $^ $@ && chmod 755 $@; \\');
+ T($F, '@ if $(BSD_INSTALL_LIB) $^ $@; \\');
T($F, ' then \\');
if ($OS ne 'mac') {
T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
. '$(patsubst %$(VERSION_SHLX),%$(SHLX),$@); \\');
}
- if ($OS eq 'linux') {
+ if ($OS eq 'linux' || $OS eq 'bsd') {
T($F, ' ln -s $(@F) $(patsubst %$(VERSION),%$(MAJVERS),$@); \\');
} elsif ($OS eq 'mac') {
T($F, ' ln -sf $(@F) '
@@ -1124,7 +1142,7 @@ EndText
L($F, '$(INST_BINDIR)/%$(VERSION_EXEX): $(BINDIR)/%$(VERSION_EXEX)');
T($F, '@ echo -n "installing \'$(@F)\'... "');
- T($F, '@ if cp $^ $@ && chmod 755 $@; \\');
+ T($F, '@ if $(BSD_INSTALL_PROGRAM) $^ $@; \\');
T($F, ' then \\');
T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
. '$(patsubst %$(VERSION_EXEX),%$(EXEX),$@); \\');
@@ -1406,7 +1424,7 @@ sub find_in_dir {
++$found;
}
if (! $found) {
- my $libdir = File::Spec->catdir($dir, 'lib' . $BITS);
+ my $libdir = File::Spec->catdir($dir, 'lib');
my $f = File::Spec->catdir($libdir, $lib);
print "\tchecking $f\n\t" if ($OPT{'debug'});
if (-e $f) {
@@ -1628,12 +1646,12 @@ sub find_lib {
sub check_compiler {
my ($t, $n, $I, @l) = @_;
- my $tool = $TOOLS;
+ my $tool = $CC;
if ($t eq 'L') {
print "checking for $n library... ";
} elsif ($t eq 'O') {
- if ($tool && ($tool =~ /gcc$/ || $tool =~ /g\+\+$/)) {
+ if ($tool && ($tool =~ /gcc/ || $tool =~ /g\+\+/)) {
print "checking whether $tool accepts $n... ";
} else {
return;
@@ -1706,7 +1724,7 @@ sub check_compiler {
}
}
my $gcc = "| $tool -xc $flags " . ($I ? "-I$I " : ' ')
- . ($l ? "-L$l " : ' ') . "- $library";
+ . ($l ? "-L$l " : ' ') . "-o a.out - $library";
$gcc .= ' 2> /dev/null' unless ($OPT{'debug'});
open GCC, $gcc or last;

20
biology/sra-tools/files/patch-ncbi-vdb_setup_os-arch.prl
View File

@ -1,20 +0,0 @@
--- ncbi-vdb/setup/os-arch.prl.orig 2021-03-15 18:16:43 UTC
+++ ncbi-vdb/setup/os-arch.prl
@@ -11,6 +11,8 @@ sub OsArch {
chomp $UNAME;
if ($UNAME =~ /Darwin/) {
$HOST_OS = 'mac';
+ } elsif ($UNAME =~ /.*BSD/) {
+ $HOST_OS = 'bsd';
} elsif ($UNAME =~ /Linux/) {
$HOST_OS = 'linux';
} elsif ($UNAME =~ /SunOS/) {
@@ -48,6 +50,8 @@ sub OsArch {
$HOST_ARCH = 'i386';
}
} elsif ($MARCH =~ /x86_64/) {
+ $HOST_ARCH = 'x86_64';
+ } elsif ($MARCH =~ /amd64/) {
$HOST_ARCH = 'x86_64';
} elsif ($MARCH =~ /i86pc/) {
$HOST_ARCH = 'x86_64';

12
biology/sra-tools/files/patch-ncbi-vdb_test_kfg_kfgtest.cpp
View File

@ -1,11 +1,11 @@
--- ncbi-vdb/test/kfg/kfgtest.cpp.orig 2019-08-20 18:27:10 UTC
--- ncbi-vdb/test/kfg/kfgtest.cpp.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/test/kfg/kfgtest.cpp
@@ -280,6 +280,8 @@ FIXTURE_TEST_CASE(predef_OS, KfgFixture)
@@ -282,6 +282,8 @@ FIXTURE_TEST_CASE(predef_ARCHBITS, KfgFixture)
FIXTURE_TEST_CASE(predef_OS, KfgFixture)
{
CreateAndLoad(GetName(), "var=$(OS)\n");
+ #if BSD
+ #define OS "bsd"
#if LINUX
#define OS "linux"
+ #elif BSD
+ #define OS "bsd"
#elif SUN
#define OS "sun"
#elif MAC

8
biology/sra-tools/files/patch-ncbi-vdb_test_klib_printf-test.c
View File

@ -1,11 +1,11 @@
--- ncbi-vdb/test/klib/printf-test.c.orig 2019-08-20 18:27:10 UTC
--- ncbi-vdb/test/klib/printf-test.c.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/test/klib/printf-test.c
@@ -503,7 +503,7 @@ rc_t run ( const char *progname )
@@ -504,7 +504,7 @@ rc_t run ( const char *progname )
if ( rc == 0 )
{
rc = make_initial_test ( field_width, precision, " ", "s", "Kurt is having a fit" );
-#if !defined(__SunOS) && !defined(__sun__)
+#if !defined(__SunOS) && !defined(__sun__) && !defined(__FreeBSD__)
/* Solaris printf doesn't cope with NULLs */
rc = make_initial_test ( field_width, precision, " ", "s", NULL );
#endif
#if 0
/* The standard says this result is undefined, we shouldn't test for it, it is not consistent */

19
biology/sra-tools/files/patch-ncbi-vdb_test_kns_Makefile
View File

@ -1,19 +0,0 @@
--- ncbi-vdb/test/kns/Makefile.orig 2021-03-15 18:16:43 UTC
+++ ncbi-vdb/test/kns/Makefile
@@ -25,7 +25,7 @@
default: runtests
-runtests: run-tests run-test-proxy-with-scheme
+runtests:
TOP ?= $(abspath ../..)
MODULE = test/kns
@@ -133,6 +133,7 @@ $(TEST_BINDIR)/test-kns: $(KNSTEST_OBJ)
$(LP) --exe -o $@ $^ $(KNSTEST_LIB)
kns: test-kns
+ if [ ! -d $(HOME)/.ncbi ]; then mkdir $(HOME)/.ncbi; fi
$(TEST_BINDIR)/test-kns #-l=all
#----------------------------------------------------------------

11
biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies.cpp
View File

@ -1,11 +0,0 @@
--- ncbi-vdb/test/vdb/test-dependencies.cpp.orig 2019-08-20 18:27:10 UTC
+++ ncbi-vdb/test/vdb/test-dependencies.cpp
@@ -115,7 +115,7 @@ class EmptyFixture : public DepFixture { (public)
class RefseqFixture : public DepFixture {
- #if LINUX
+ #if LINUX || BSD
#define PATH "kfg/linux"
#elif MAC
#define PATH "kfg/mac"

12
biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies__dflt.cpp Normal file
View File

@ -0,0 +1,12 @@
--- ncbi-vdb/test/vdb/test-dependencies_dflt.cpp.orig 2023-07-10 16:13:36 UTC
+++ ncbi-vdb/test/vdb/test-dependencies_dflt.cpp
@@ -139,6 +139,9 @@ class EmptyFixture : public DepFixture { (public)
class RefseqFixture : public DepFixture {
+ #if BSD
+ // FIXME: Should there be a separate kfg/freebsd?
+ #define PATH "kfg/linux"
#if LINUX
#define PATH "kfg/linux"
#elif MAC

11
biology/sra-tools/files/patch-ncbi-vdb_test_vfs_redirect-rejected-names-cgi-http-to-https.cpp
View File

@ -1,11 +0,0 @@
--- ncbi-vdb/test/vfs/redirect-rejected-names-cgi-http-to-https.cpp.orig 2017-07-14 21:55:36 UTC
+++ ncbi-vdb/test/vfs/redirect-rejected-names-cgi-http-to-https.cpp
@@ -148,7 +148,7 @@ struct Test : protected ncbi :: NK :: Sh
TEST_CASE(TEST) {
-#define RESOLVER_CGI_HEAD "test.ncbi.nlm.nih."
+#define RESOLVER_CGI_HEAD "www.ncbi.nlm.nih."
#ifdef VDB_3162
#else

13
biology/sra-tools/files/patch-setup_install.perl
View File

@ -1,13 +0,0 @@
--- setup/install.perl.orig 2021-03-15 18:25:25 UTC
+++ setup/install.perl
@@ -1283,8 +1283,8 @@ sub prepare {
' $_{INST_JARDIR } = "$_{PREFIX}/jar"; ' .
' $_{INST_SHAREDIR} = "$_{PREFIX}/share"; ' .
' $_{INCDIR } = "$Bin/../include"; ' .
- ' $_{LIBDIR64 } = "$Bin/../lib64"; ' .
- ' $_{LIBDIR32 } = "$Bin/../lib32"; ';
+ ' $_{LIBDIR64 } = "$Bin/../lib"; ' .
+ ' $_{LIBDIR32 } = "$Bin/../lib"; ';
if ($HAVE{TWO_LIBS}) {
$code .=
'$_{INST_NGSLIBDIR} = "' . "$root/usr/local/ngs/ngs-sdk/lib\";"

121
biology/sra-tools/files/patch-setup_konfigure.perl
View File

@ -1,121 +0,0 @@
--- setup/konfigure.perl.orig 2021-03-15 18:25:25 UTC
+++ setup/konfigure.perl
@@ -204,7 +204,7 @@ print "checking system type... " unless ($AUTORUN);
my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
println $OSTYPE unless ($AUTORUN);
-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
+unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win' || $OSTYPE =~ /freebsd/i) {
println "configure: error: unsupported system '$OSTYPE'";
exit 1;
}
@@ -225,7 +225,7 @@ if ($OS eq 'linux') {
print "checking machine architecture... " unless ($AUTORUN);
println $MARCH unless ($AUTORUN);
-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) {
+unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) {
println "configure: error: unsupported architecture '$OSTYPE':'$MARCH'";
exit 1;
}
@@ -310,7 +310,7 @@ print "checking for supported architecture... " unless
my $BITS;
-if ($MARCH =~ /x86_64/i) {
+if ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i) {
$BITS = 64;
} elsif ($MARCH eq 'fat86') {
$BITS = '32_64';
@@ -337,6 +337,16 @@ if ($OSTYPE =~ /linux/i) {
$OSINC = 'unix';
$TOOLS = 'gcc' unless ($TOOLS);
$PYTHON = 'python';
+} elsif ($OSTYPE =~ /freebsd/i) {
+ $LPFX = 'lib';
+ $OBJX = 'o';
+ $LOBX = 'pic.o';
+ $LIBX = 'a';
+ $SHLX = 'so';
+ $EXEX = '';
+ $OSINC = 'unix';
+ $TOOLS = 'clang' unless ($TOOLS);
+ $PYTHON = 'python';
} elsif ($OSTYPE =~ /darwin/i) {
$LPFX = 'lib';
$OBJX = 'o';
@@ -512,7 +522,7 @@ foreach my $href (DEPENDS()) {
$I = $t if (-e $t);
}
push ( @L, File::Spec->catdir($OPT{$o}, 'lib') );
- push ( @L, File::Spec->catdir($OPT{$o}, 'lib64') );
+ #push ( @L, File::Spec->catdir($OPT{$o}, 'lib64') );
}
my ($i, $l) = find_lib($_, $I, @L);
if (defined $i || $l) {
@@ -934,7 +944,7 @@ EndText
if ($PKG{LNG} eq 'C') {
if ($TOOLS =~ /clang/i) {
L($F, 'SONAME = -install_name ' .
- '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
+ '$(INST_LIBDIR)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
L($F, ' -compatibility_version $(MAJMIN) -current_version $(VERSION) \\');
L($F, ' -flat_namespace -undefined suppress');
} else {
@@ -1043,7 +1053,7 @@ EndText
L($F, '# directory rules');
if ($PKG{LNG} eq 'C') {
L($F, '$(BINDIR) $(LIBDIR) $(ILIBDIR) '
- . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):');
+ . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR):');
T($F, 'mkdir -p $@');
} elsif ($PKG{LNG} eq 'JAVA') {
# test if we have jni header path
@@ -1076,7 +1086,7 @@ EndText
if ($OS eq 'linux' || $OS eq 'mac') {
L($F, '# installation rules');
L($F,
- '$(INST_LIBDIR)$(BITS)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
+ '$(INST_LIBDIR)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
T($F, '@ echo -n "installing \'$(@F)\'... "');
T($F, '@ if cp $^ $@ && chmod 644 $@; \\');
T($F, ' then \\');
@@ -1087,7 +1097,7 @@ EndText
T($F, ' ln -s $(patsubst %$(VERSION),%$(MAJVERS),$(@F)) '
. '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@); \\');
T($F, ' ln -s $(patsubst %$(VERSION_LIBX),%$(LIBX),$(@F)) ' .
- '$(INST_LIBDIR)$(BITS)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
+ '$(INST_LIBDIR)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
. ' \\');
T($F, ' echo success; \\');
T($F, ' else \\');
@@ -1097,7 +1107,7 @@ EndText
L($F);
L($F,
- '$(INST_LIBDIR)$(BITS)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
+ '$(INST_LIBDIR)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
T($F, '@ echo -n "installing \'$(@F)\'... "');
T($F, '@ if cp $^ $@ && chmod 755 $@; \\');
T($F, ' then \\');
@@ -1168,9 +1178,9 @@ EndText
print $F " \$_{INCDIR } = '" . expand("$Bin/.." ) . "';\n";
if ($PKG{LNG} ne 'PYTHON') {
print $F " \$_{BINDIR$BITS} = '" . expand($E_BINDIR ) . "';\n";
- print $F " \$_{LIBDIR$BITS} = '" . expand($E_LIBDIR ) . "';\n";
+ print $F " \$_{LIBDIR} = '" . expand($E_LIBDIR ) . "';\n";
} elsif ($OPT{PYTHON_LIB_PATH}) {
- print $F " \$_{LIBDIR$BITS} = '$OPT{PYTHON_LIB_PATH}';\n";
+ print $F " \$_{LIBDIR} = '$OPT{PYTHON_LIB_PATH}';\n";
}
print $F " \$_{OTHER_PREFIX } = '$PKG{UPATH}';\n";
print $F " \$_{PREFIX } = '$OPT{'prefix'}';\n";
@@ -1406,7 +1416,7 @@ sub find_in_dir {
++$found;
}
if (! $found) {
- my $libdir = File::Spec->catdir($dir, 'lib' . $BITS);
+ my $libdir = File::Spec->catdir($dir, 'lib');
my $f = File::Spec->catdir($libdir, $lib);
print "\tchecking $f\n\t" if ($OPT{'debug'});
if (-e $f) {

10
biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c
View File

@ -1,10 +0,0 @@
--- tools/bam-loader/loader-imp.c.orig 2021-06-20 16:59:47 UTC
+++ tools/bam-loader/loader-imp.c
@@ -71,6 +71,7 @@
#include <sysalloc.h>
#include <atomic32.h>
+#include <sys/stat.h>
#include <unistd.h>
#include <fcntl.h>
#include <sys/mman.h>

11
biology/sra-tools/files/patch-tools_copycat_Makefile
View File

@ -1,11 +0,0 @@
--- tools/copycat/Makefile.orig 2021-06-20 17:45:49 UTC
+++ tools/copycat/Makefile
@@ -92,7 +92,7 @@ COPYCAT_LIB = \
-stk-version \
-sncbi-vdb \
-skff \
- -smagic-static
+ -smagic
$(BINDIR)/copycat: $(COPYCAT_OBJ)

16
biology/sra-tools/files/patch-tools_driver-tool_Makefile
View File

@ -1,16 +0,0 @@
--- tools/driver-tool/Makefile.orig 2021-03-15 18:25:25 UTC
+++ tools/driver-tool/Makefile
@@ -97,7 +97,12 @@ SRATOOLS_OBJ = \
SRATOOLS_LIB = \
-sncbi-vdb \
-sjson \
- -lm
+ -lepoll-shim \
+ -lmbedtls \
+ -lm \
+ -lexecinfo \
+ -lz \
+ -lbz2
$(BINDIR)/sratools: $(SRATOOLS_OBJ) $(ILIBDIR)/libjson.$(LIBX)
$(LP) --exe --vers $(SRCDIR)/../../shared/toolkit.vers -o $@ $^ $(SRATOOLS_LIB)

13
biology/sra-tools/files/patch-tools_driver-tool_cmdline.cpp
View File

@ -1,13 +0,0 @@
--- tools/driver-tool/cmdline.cpp.orig 2021-04-21 19:42:12 UTC
+++ tools/driver-tool/cmdline.cpp
@@ -50,6 +50,10 @@
#define environ (*_NSGetEnviron())
#endif
+#if defined(__FreeBSD__)
+extern char **environ;
+#endif
+
#define TRACE( lvl, ... ) /* ignore */
namespace ncbi

11
biology/sra-tools/files/patch-tools_driver-tool_utf8proc_Makefile
View File

@ -1,11 +0,0 @@
--- tools/driver-tool/utf8proc/Makefile.orig 2021-04-29 14:50:48 UTC
+++ tools/driver-tool/utf8proc/Makefile
@@ -79,7 +79,7 @@ libutf8proc.a: utf8proc.o
libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH): utf8proc.o
$(CC) $(LDFLAGS) -shared -o $@ -Wl,-soname -Wl,libutf8proc.so.$(MAJOR) utf8proc.o
- chmod a-x $@
+ # FIX .so build so this will work: chmod a-x $@
libutf8proc.so: libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH)
ln -f -s libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH) $@

20
biology/sra-tools/files/patch-tools_external_driver-tool_file-path.posix.cpp Normal file
View File

@ -0,0 +1,20 @@
--- tools/external/driver-tool/file-path.posix.cpp.orig 2023-07-10 16:23:35 UTC
+++ tools/external/driver-tool/file-path.posix.cpp
@@ -193,7 +193,16 @@ static char const *find_executable_path(char const *co
FilePath FilePath::fullPathToExecutable(char const *const *const argv, char const *const *const envp, char const *const *const extra)
{
char const *path;
-#if LINUX
+// Assume sra-tools is installed by FreeBSD ports. FreeBSD users
+// don't often install software by other means. Default prefix
+// is /usr/local, but this can be overridden by the user building
+// the port. The port can replace /usr/local using sed if that's the
+// case.
+#if BSD
+ char full_path[PATH_MAX];
+ snprintf(full_path, PATH_MAX, "/usr/local/bin/%s", argv[0]);
+ path = full_path;
+#elif LINUX
path = "/proc/self/exe";
#elif MAC
path = find_executable_path(extra, argv[0]);

25
biology/sra-tools/files/patch-tools_external_driver-tool_sratools.cpp Normal file
View File

@ -0,0 +1,25 @@
--- tools/external/driver-tool/sratools.cpp.orig 2023-07-10 16:23:35 UTC
+++ tools/external/driver-tool/sratools.cpp
@@ -420,6 +420,7 @@ static int main(CommandLine const &argv)
enableLogging(argv.toolName.c_str());
#endif
LOG(7) << "executable path: " << (std::string)argv.fullPathToExe << std::endl;
+ // std::cerr << "executable path: " << (std::string)argv.fullPathToExe << std::endl;
config = new Config();
struct Defer { ~Defer() { delete config; config = nullptr; } } freeConfig;
@@ -576,6 +577,14 @@ static int main(CommandLine const &argv)
}
} // namespace sratools
+
+#if BSD
+int main(int argc, char *argv[], char *envp[])
+{
+ auto const invocation = CommandLine(argc, argv, envp, nullptr);
+ return sratools::main(invocation);
+}
+#endif
#if MAC
int main(int argc, char *argv[], char *envp[], char *apple[])

20
biology/sra-tools/files/patch-tools_external_vdb-config_tui_CMakeLists.txt Normal file
View File

@ -0,0 +1,20 @@
--- tools/external/vdb-config/tui/CMakeLists.txt.orig 2023-07-10 16:23:35 UTC
+++ tools/external/vdb-config/tui/CMakeLists.txt
@@ -25,6 +25,7 @@
include_directories( ${CMAKE_CURRENT_SOURCE_DIR}/.. )
set ( UNIX_SRC unix/systui.c )
+set ( BSD_SRC bsd/systui.c )
set ( LINUX_SRC linux/systui.c )
set ( MAC_SRC bsd/systui.c )
set ( WIN_SRC win/systui.c )
@@ -32,6 +33,9 @@ set ( WIN_SRC win/systui.c )
if ( "windows" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${WIN_SRC} )
#include_directories( win )
+elseif( "bsd" STREQUAL ${OS} )
+ set ( OS_SPECIFIC_SRC ${BSD_SRC} )
+ #include_directories( unix )
elseif( "linux" STREQUAL ${OS} )
set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
#include_directories( unix )

11
biology/sra-tools/files/patch-tools_fastq-loader_spot-assembler.c
View File

@ -1,11 +0,0 @@
--- tools/fastq-loader/spot-assembler.c.orig 2021-06-20 17:00:29 UTC
+++ tools/fastq-loader/spot-assembler.c
@@ -26,6 +26,8 @@
#include "spot-assembler.h"
+#include <sys/stat.h>
+
#include <klib/status.h>
#include <klib/printf.h>

17
biology/sra-tools/files/patch-tools_loaders_fastq-loader_spot-assembler.c Normal file
View File

@ -0,0 +1,17 @@
--- tools/loaders/fastq-loader/spot-assembler.c.orig 2023-08-08 12:26:35 UTC
+++ tools/loaders/fastq-loader/spot-assembler.c
@@ -1,3 +1,4 @@
+
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -25,6 +26,9 @@
*/
#include "spot-assembler.h"
+
+// FIXME: Unsure if this is still necessary
+#include <sys/stat.h>
#include <klib/status.h>
#include <klib/printf.h>

13
biology/sra-tools/files/patch-tools_sra-sort_Makefile
View File

@ -1,13 +0,0 @@
--- tools/sra-sort/Makefile.orig 2021-06-20 22:24:20 UTC
+++ tools/sra-sort/Makefile
@@ -135,7 +135,9 @@ DBB_OBJ = \
$(addsuffix .$(OBJX),$(DBB_SRC))
DBB_LIB = \
- -lncbi-vdb \
+ -sncbi-vdb \
$(BINDIR)/dump-blob-boundaries: $(DBB_OBJ)
+ @echo "LD = ${LD}"
+ @echo "DBB_LIB = ${DBB_LIB}"
$(LD) --exe -o $@ $^ $(DBB_LIB)

13
biology/sra-tools/files/patch-tools_util_validate-names4.c
View File

@ -1,13 +0,0 @@
--- tools/util/validate-names4.c.orig 2021-06-20 17:53:25 UTC
+++ tools/util/validate-names4.c
@@ -30,8 +30,8 @@
#include <klib/rc.h> /* RC */
#include <vfs/path.h> /* VPath */
-#include "../../../ncbi-vdb/libs/vfs/json-response.h" /* Response4Make4 */
-#include "../../../ncbi-vdb/libs/vfs/services-priv.h"/*KServiceGetKSrvResponse*/
+#include "../libs/vfs/json-response.h" /* Response4Make4 */
+#include "../libs/vfs/services-priv.h"/*KServiceGetKSrvResponse*/
#define RELEASE(type, obj) do { rc_t rc2 = type##Release(obj); \
if (rc2 && !rc) { rc = rc2; } obj = NULL; } while (false)

3
biology/sra-tools/pkg-descr
View File

@ -1,16 +1,13 @@
SRA tools is a toolkit for using data in the INSDC Sequence Read Archives.
SRAs operated by International Nucleotide Sequence Database Collaboration
houses sequence reads and alignments generated by "next-gen" sequencers.
SRA tools allows conversion of .sra files, which INSDC SRAs maintain,
from/to other formats that the 'next-gen' sequenecers generate including:
* csfasta/csqual (ABI SOLiD)
* fastq (and fasta for writing)
* hdf5 (PacBio, reading only)
* qseq (older Illumina)
* sam (writing only) / bam (reading only)
* sff
The toolkit uses NCBI-VDB back-end enabling seamless access to remote SRA data
and local SRA files.

293
biology/sra-tools/pkg-plist
View File

@ -1,57 +1,282 @@
bin/abi-dump
bin/abi-load
bin/align-cache
bin/abi-dump.3
bin/abi-dump.3.0.6
bin/align-info
bin/bam-load
bin/align-info.3
bin/align-info.3.0.6
bin/cache-mgr
bin/ccextract
bin/cg-load
bin/cache-mgr.3
bin/cache-mgr.3.0.6
bin/check-corrupt
bin/copycat
bin/check-corrupt.3
bin/check-corrupt.3.0.6
bin/fasterq-dump
bin/fasterq-dump-orig.3.0.6
bin/fasterq-dump.3
bin/fasterq-dump.3.0.6
bin/fastq-dump
bin/fastq-load
bin/helicos-load
bin/fastq-dump-orig.3.0.6
bin/fastq-dump.3
bin/fastq-dump.3.0.6
bin/illumina-dump
bin/illumina-load
bin/kar
bin/kar+
bin/kar+meta
bin/kdb-index
bin/illumina-dump.3
bin/illumina-dump.3.0.6
bin/kdbmeta
bin/kget
bin/latf-load
bin/make-read-filter
bin/md5cp
bin/kdbmeta.3
bin/kdbmeta.3.0.6
bin/ngs-pileup
bin/pacbio-correct
bin/pacbio-loadxml
bin/ngs-pileup.3
bin/ngs-pileup.3.0.6
bin/prefetch
bin/qual-recalib-stat
bin/prefetch-orig.3.0.6
bin/prefetch.3
bin/prefetch.3.0.6
bin/rcexplain
bin/read-filter-redact
bin/rcexplain.3
bin/rcexplain.3.0.6
bin/ref-variation
bin/ref-variation.3
bin/ref-variation.3.0.6
bin/sam-dump
bin/samview
bin/schema-replace
bin/sam-dump-orig.3.0.6
bin/sam-dump.3
bin/sam-dump.3.0.6
bin/sff-dump
bin/sff-load
bin/sff-dump.3
bin/sff-dump.3.0.6
bin/sra-info
bin/sra-info.3
bin/sra-info.3.0.6
bin/sra-pileup
bin/sra-sort
bin/sra-sort-cg
bin/sra-pileup-orig.3.0.6
bin/sra-pileup.3
bin/sra-pileup.3.0.6
bin/sra-search
bin/sra-search.3
bin/sra-search.3.0.6
bin/sra-stat
bin/sra-stat.3
bin/sra-stat.3.0.6
bin/srapath
bin/srapath-orig.3.0.6
bin/srapath.3
bin/srapath.3.0.6
bin/sratools
bin/srf-load
bin/test-read-write-cursor
bin/sratools.3
bin/sratools.3.0.6
bin/test-sra
bin/test-sra.3
bin/test-sra.3.0.6
bin/var-expand
bin/var-expand.3
bin/var-expand.3.0.6
bin/vdb-config
bin/vdb-copy
bin/vdb-config.3
bin/vdb-config.3.0.6
bin/vdb-decrypt
bin/vdb-diff
bin/vdb-decrypt.3
bin/vdb-decrypt.3.0.6
bin/vdb-dump
bin/vdb-dump-orig.3.0.6
bin/vdb-dump.3
bin/vdb-dump.3.0.6
bin/vdb-encrypt
bin/vdb-lock
bin/vdb-passwd
bin/vdb-sql
bin/vdb-unlock
bin/vdb-encrypt.3
bin/vdb-encrypt.3.0.6
bin/vdb-validate
bin/vdb-validate.3
bin/vdb-validate.3.0.6
include/ncbi-vdb/NGS.hpp
include/ngs/Alignment.hpp
include/ngs/AlignmentIterator.hpp
include/ngs/ErrorMsg.hpp
include/ngs/Fragment.hpp
include/ngs/FragmentIterator.hpp
include/ngs/Package.hpp
include/ngs/Pileup.hpp
include/ngs/PileupEvent.hpp
include/ngs/PileupEventIterator.hpp
include/ngs/PileupIterator.hpp
include/ngs/Read.hpp
include/ngs/ReadCollection.hpp
include/ngs/ReadGroup.hpp
include/ngs/ReadGroupIterator.hpp
include/ngs/ReadIterator.hpp
include/ngs/Reference.hpp
include/ngs/ReferenceIterator.hpp
include/ngs/ReferenceSequence.hpp
include/ngs/Statistics.hpp
include/ngs/StringRef.hpp
include/ngs/adapter/AlignmentItf.hpp
include/ngs/adapter/ErrorMsg.hpp
include/ngs/adapter/FragmentItf.hpp
include/ngs/adapter/PileupEventItf.hpp
include/ngs/adapter/PileupItf.hpp
include/ngs/adapter/ReadCollectionItf.hpp
include/ngs/adapter/ReadGroupItf.hpp
include/ngs/adapter/ReadItf.hpp
include/ngs/adapter/Refcount.hpp
include/ngs/adapter/ReferenceItf.hpp
include/ngs/adapter/ReferenceSequenceItf.hpp
include/ngs/adapter/StatisticsItf.hpp
include/ngs/adapter/StringItf.hpp
include/ngs/adapter/defs.h
include/ngs/inl/Alignment.hpp
include/ngs/inl/AlignmentIterator.hpp
include/ngs/inl/Fragment.hpp
include/ngs/inl/FragmentIterator.hpp
include/ngs/inl/Package.hpp
include/ngs/inl/Pileup.hpp
include/ngs/inl/PileupEvent.hpp
include/ngs/inl/PileupEventIterator.hpp
include/ngs/inl/PileupIterator.hpp
include/ngs/inl/Read.hpp
include/ngs/inl/ReadCollection.hpp
include/ngs/inl/ReadGroup.hpp
include/ngs/inl/ReadGroupIterator.hpp
include/ngs/inl/ReadIterator.hpp
include/ngs/inl/Reference.hpp
include/ngs/inl/ReferenceIterator.hpp
include/ngs/inl/ReferenceSequence.hpp
include/ngs/inl/Statistics.hpp
include/ngs/inl/StringRef.hpp
include/ngs/itf/AlignmentItf.h
include/ngs/itf/AlignmentItf.hpp
include/ngs/itf/ErrBlock.h
include/ngs/itf/ErrBlock.hpp
include/ngs/itf/ErrorMsg.hpp
include/ngs/itf/FragmentItf.h
include/ngs/itf/FragmentItf.hpp
include/ngs/itf/PackageItf.hpp
include/ngs/itf/PileupEventItf.h
include/ngs/itf/PileupEventItf.hpp
include/ngs/itf/PileupItf.h
include/ngs/itf/PileupItf.hpp
include/ngs/itf/ReadCollectionItf.h
include/ngs/itf/ReadCollectionItf.hpp
include/ngs/itf/ReadGroupItf.h
include/ngs/itf/ReadGroupItf.hpp
include/ngs/itf/ReadItf.h
include/ngs/itf/ReadItf.hpp
include/ngs/itf/Refcount.h
include/ngs/itf/Refcount.hpp
include/ngs/itf/ReferenceItf.h
include/ngs/itf/ReferenceItf.hpp
include/ngs/itf/ReferenceSequenceItf.h
include/ngs/itf/ReferenceSequenceItf.hpp
include/ngs/itf/StatisticsItf.h
include/ngs/itf/StatisticsItf.hpp
include/ngs/itf/StringItf.h
include/ngs/itf/StringItf.hpp
include/ngs/itf/VTable.h
include/ngs/itf/VTable.hpp
include/ngs/itf/defs.h
include/ngs/unix/arm64/atomic32.h
include/ngs/unix/fat86/atomic32.h
include/ngs/unix/i386/atomic32.h
include/ngs/unix/x86_64/atomic32.h
include/ngs/win/atomic32.h
include/ngs/win/stdbool.h
jar/ngs-doc.jar
jar/ngs-examples.jar
jar/ngs-java.jar
jar/ngs-src.jar
lib64/libncbi-ngs-c++-static.a
lib64/libncbi-ngs-c++.a
lib64/libncbi-ngs-c++.a.3
lib64/libncbi-ngs-c++.a.3.0.6
lib64/libncbi-ngs-static.a
lib64/libncbi-ngs.a
lib64/libncbi-ngs.a.3
lib64/libncbi-ngs.a.3.0.6
lib64/libncbi-ngs.so
lib64/libncbi-ngs.so.3
lib64/libncbi-ngs.so.3.0.6
lib64/libngs-c++-static.a
lib64/libngs-c++.a
lib64/libngs-c++.a.3
lib64/libngs-c++.a.3.0.6
lib64/libngs-c++.so
lib64/libngs-c++.so.3
lib64/libngs-c++.so.3.0.6
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignSliceTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DumpReferenceFASTA.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/FragTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/PileupTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/RefTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/expected.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/Makefile
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/AlignSliceTest.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/AlignTest.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/DumpReferenceFASTA.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/FragTest.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/PileupTest.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/ReadGroupTest.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/RefTest.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/expected.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/AlignSliceTest.py
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/AlignTest.py
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/FragTest.py
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/Makefile
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/PileupTest.py
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/RefTest.py
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/expected.txt
%%JAVASHAREDIR%%doc/ngs-doc/allclasses-index.html
%%JAVASHAREDIR%%doc/ngs-doc/allpackages-index.html
%%JAVASHAREDIR%%doc/ngs-doc/constant-values.html
%%JAVASHAREDIR%%doc/ngs-doc/element-list
%%JAVASHAREDIR%%doc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html
%%JAVASHAREDIR%%doc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html
%%JAVASHAREDIR%%doc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html
%%JAVASHAREDIR%%doc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html
%%JAVASHAREDIR%%doc/ngs-doc/help-doc.html
%%JAVASHAREDIR%%doc/ngs-doc/index-all.html
%%JAVASHAREDIR%%doc/ngs-doc/index.html
%%JAVASHAREDIR%%doc/ngs-doc/jquery-ui.overrides.css
%%JAVASHAREDIR%%doc/ngs-doc/legal/ADDITIONAL_LICENSE_INFO
%%JAVASHAREDIR%%doc/ngs-doc/legal/ASSEMBLY_EXCEPTION
%%JAVASHAREDIR%%doc/ngs-doc/legal/LICENSE
%%JAVASHAREDIR%%doc/ngs-doc/legal/jquery.md
%%JAVASHAREDIR%%doc/ngs-doc/legal/jqueryUI.md
%%JAVASHAREDIR%%doc/ngs-doc/member-search-index.js
%%JAVASHAREDIR%%doc/ngs-doc/module-search-index.js
%%JAVASHAREDIR%%doc/ngs-doc/ngs/Alignment.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/AlignmentIterator.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/ErrorMsg.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/Fragment.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/FragmentIterator.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/Package.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/Pileup.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/PileupEvent.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/PileupEventIterator.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/PileupIterator.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/Read.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/ReadCollection.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/ReadGroup.html
%%JAVASHAREDIR%%doc/ngs-doc/ngs/ReadGroupIterator.html
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3
cad/nvc/Makefile
View File

@ -1,6 +1,7 @@
PORTNAME= nvc
DISTVERSIONPREFIX= r
DISTVERSION= 1.10.1
PORTREVISION= 1
CATEGORIES= cad
MAINTAINER= yuri@FreeBSD.org
@ -56,7 +57,7 @@ CONFIGURE_CMD= ${WRKSRC}/configure
.include <bsd.port.options.mk>
.if ${ARCH} == "i386" || ${ARCH} == powerpc64 # see the bug#268319 for the LTO failure on i386
.if ${ARCH} == "i386" # see the bug#268319 for the LTO failure on i386
CONFIGURE_ARGS+= --disable-lto # workaround for https://github.com/nickg/nvc/issues/579 (undefined symbol: _GLOBAL_OFFSET_TABLE_, see error: undefined symbol: _GLOBAL_OFFSET_TABLE_)
.endif

51
cad/svlint/Makefile
View File

@ -1,7 +1,6 @@
PORTNAME= svlint
DISTVERSIONPREFIX= v
DISTVERSION= 0.8.0
PORTREVISION= 1
DISTVERSION= 0.9.0
CATEGORIES= cad devel
MAINTAINER= yuri@FreeBSD.org
@ -16,31 +15,39 @@ USES= cargo
USE_GITHUB= yes
GH_ACCOUNT= dalance
CARGO_CRATES= aho-corasick-1.0.2 \
anyhow-1.0.71 \
CARGO_CRATES= aho-corasick-1.0.3 \
anyhow-1.0.72 \
atty-0.2.14 \
autocfg-1.1.0 \
bitflags-1.3.2 \
bitflags-2.3.3 \
bytecount-0.6.3 \
cc-1.0.82 \
cfg-if-1.0.0 \
clap-3.2.25 \
clap_complete-3.2.5 \
clap_derive-3.2.25 \
clap_lex-0.2.4 \
colored-2.0.0 \
colored-2.0.4 \
dirs-next-2.0.0 \
dirs-sys-next-0.1.2 \
enquote-1.1.0 \
equivalent-1.0.0 \
equivalent-1.0.1 \
errno-0.3.2 \
errno-dragonfly-0.1.2 \
getrandom-0.2.10 \
hashbrown-0.12.3 \
hashbrown-0.14.0 \
heck-0.4.1 \
hermit-abi-0.1.19 \
hermit-abi-0.3.2 \
indexmap-1.9.3 \
indexmap-2.0.0 \
is-terminal-0.4.9 \
lazy_static-1.4.0 \
libc-0.2.147 \
libloading-0.8.0 \
linux-raw-sys-0.4.5 \
memchr-2.5.0 \
minimal-lexical-0.2.1 \
nom-7.1.3 \
@ -56,16 +63,18 @@ CARGO_CRATES= aho-corasick-1.0.2 \
os_str_bytes-6.5.1 \
proc-macro-error-1.0.4 \
proc-macro-error-attr-1.0.4 \
proc-macro2-1.0.63 \
quote-1.0.28 \
proc-macro2-1.0.66 \
quote-1.0.32 \
redox_syscall-0.2.16 \
redox_users-0.4.3 \
regex-1.8.4 \
regex-syntax-0.7.2 \
rustversion-1.0.12 \
regex-1.9.3 \
regex-automata-0.3.6 \
regex-syntax-0.7.4 \
rustix-0.38.7 \
rustversion-1.0.14 \
same-file-1.0.6 \
serde-1.0.164 \
serde_derive-1.0.164 \
serde-1.0.183 \
serde_derive-1.0.183 \
serde_regex-1.1.0 \
serde_spanned-0.6.3 \
str-concat-0.2.0 \
@ -78,16 +87,16 @@ CARGO_CRATES= aho-corasick-1.0.2 \
sv-parser-pp-0.13.1 \
sv-parser-syntaxtree-0.13.1 \
syn-1.0.109 \
syn-2.0.22 \
syn-2.0.28 \
term-0.7.0 \
termcolor-1.2.0 \
textwrap-0.16.0 \
thiserror-1.0.40 \
thiserror-impl-1.0.40 \
toml-0.7.5 \
thiserror-1.0.44 \
thiserror-impl-1.0.44 \
toml-0.7.6 \
toml_datetime-0.6.3 \
toml_edit-0.19.11 \
unicode-ident-1.0.9 \
toml_edit-0.19.14 \
unicode-ident-1.0.11 \
version_check-0.9.4 \
walkdir-2.3.3 \
wasi-0.11.0+wasi-snapshot-preview1 \
@ -96,7 +105,7 @@ CARGO_CRATES= aho-corasick-1.0.2 \
winapi-util-0.1.5 \
winapi-x86_64-pc-windows-gnu-0.4.0 \
windows-sys-0.48.0 \
windows-targets-0.48.0 \
windows-targets-0.48.1 \
windows_aarch64_gnullvm-0.48.0 \
windows_aarch64_msvc-0.48.0 \
windows_i686_gnu-0.48.0 \
@ -104,7 +113,7 @@ CARGO_CRATES= aho-corasick-1.0.2 \
windows_x86_64_gnu-0.48.0 \
windows_x86_64_gnullvm-0.48.0 \
windows_x86_64_msvc-0.48.0 \
winnow-0.4.7
winnow-0.5.4
PLIST_FILES= bin/${PORTNAME} \
bin/mdgen

102
cad/svlint/distinfo
View File

@ -1,34 +1,44 @@
TIMESTAMP = 1687849938
SHA256 (rust/crates/aho-corasick-1.0.2.crate) = 43f6cb1bf222025340178f382c426f13757b2960e89779dfcb319c32542a5a41
SIZE (rust/crates/aho-corasick-1.0.2.crate) = 167694
SHA256 (rust/crates/anyhow-1.0.71.crate) = 9c7d0618f0e0b7e8ff11427422b64564d5fb0be1940354bfe2e0529b18a9d9b8
SIZE (rust/crates/anyhow-1.0.71.crate) = 43808
TIMESTAMP = 1691642070
SHA256 (rust/crates/aho-corasick-1.0.3.crate) = 86b8f9420f797f2d9e935edf629310eb938a0d839f984e25327f3c7eed22300c
SIZE (rust/crates/aho-corasick-1.0.3.crate) = 168361
SHA256 (rust/crates/anyhow-1.0.72.crate) = 3b13c32d80ecc7ab747b80c3784bce54ee8a7a0cc4fbda9bf4cda2cf6fe90854
SIZE (rust/crates/anyhow-1.0.72.crate) = 43837
SHA256 (rust/crates/atty-0.2.14.crate) = d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8
SIZE (rust/crates/atty-0.2.14.crate) = 5470
SHA256 (rust/crates/autocfg-1.1.0.crate) = d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa
SIZE (rust/crates/autocfg-1.1.0.crate) = 13272
SHA256 (rust/crates/bitflags-1.3.2.crate) = bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a
SIZE (rust/crates/bitflags-1.3.2.crate) = 23021
SHA256 (rust/crates/bitflags-2.3.3.crate) = 630be753d4e58660abd17930c71b647fe46c27ea6b63cc59e1e3851406972e42
SIZE (rust/crates/bitflags-2.3.3.crate) = 34320
SHA256 (rust/crates/bytecount-0.6.3.crate) = 2c676a478f63e9fa2dd5368a42f28bba0d6c560b775f38583c8bbaa7fcd67c9c
SIZE (rust/crates/bytecount-0.6.3.crate) = 12416
SHA256 (rust/crates/cc-1.0.82.crate) = 305fe645edc1442a0fa8b6726ba61d422798d37a52e12eaecf4b022ebbb88f01
SIZE (rust/crates/cc-1.0.82.crate) = 67879
SHA256 (rust/crates/cfg-if-1.0.0.crate) = baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd
SIZE (rust/crates/cfg-if-1.0.0.crate) = 7934
SHA256 (rust/crates/clap-3.2.25.crate) = 4ea181bf566f71cb9a5d17a59e1871af638180a18fb0035c92ae62b705207123
SIZE (rust/crates/clap-3.2.25.crate) = 219403
SHA256 (rust/crates/clap_complete-3.2.5.crate) = 3f7a2e0a962c45ce25afce14220bc24f9dade0a1787f185cecf96bfba7847cd8
SIZE (rust/crates/clap_complete-3.2.5.crate) = 31625
SHA256 (rust/crates/clap_derive-3.2.25.crate) = ae6371b8bdc8b7d3959e9cf7b22d4435ef3e79e138688421ec654acf8c81b008
SIZE (rust/crates/clap_derive-3.2.25.crate) = 28212
SHA256 (rust/crates/clap_lex-0.2.4.crate) = 2850f2f5a82cbf437dd5af4d49848fbdfc27c157c3d010345776f952765261c5
SIZE (rust/crates/clap_lex-0.2.4.crate) = 9652
SHA256 (rust/crates/colored-2.0.0.crate) = b3616f750b84d8f0de8a58bda93e08e2a81ad3f523089b05f1dffecab48c6cbd
SIZE (rust/crates/colored-2.0.0.crate) = 21619
SHA256 (rust/crates/colored-2.0.4.crate) = 2674ec482fbc38012cf31e6c42ba0177b431a0cb6f15fe40efa5aab1bda516f6
SIZE (rust/crates/colored-2.0.4.crate) = 23654
SHA256 (rust/crates/dirs-next-2.0.0.crate) = b98cf8ebf19c3d1b223e151f99a4f9f0690dca41414773390fc824184ac833e1
SIZE (rust/crates/dirs-next-2.0.0.crate) = 11689
SHA256 (rust/crates/dirs-sys-next-0.1.2.crate) = 4ebda144c4fe02d1f7ea1a7d9641b6fc6b580adcfa024ae48797ecdeb6825b4d
SIZE (rust/crates/dirs-sys-next-0.1.2.crate) = 10681
SHA256 (rust/crates/enquote-1.1.0.crate) = 06c36cb11dbde389f4096111698d8b567c0720e3452fd5ac3e6b4e47e1939932
SIZE (rust/crates/enquote-1.1.0.crate) = 3552
SHA256 (rust/crates/equivalent-1.0.0.crate) = 88bffebc5d80432c9b140ee17875ff173a8ab62faad5b257da912bd2f6c1c0a1
SIZE (rust/crates/equivalent-1.0.0.crate) = 6621
SHA256 (rust/crates/equivalent-1.0.1.crate) = 5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5
SIZE (rust/crates/equivalent-1.0.1.crate) = 6615
SHA256 (rust/crates/errno-0.3.2.crate) = 6b30f669a7961ef1631673d2766cc92f52d64f7ef354d4fe0ddfd30ed52f0f4f
SIZE (rust/crates/errno-0.3.2.crate) = 10424
SHA256 (rust/crates/errno-dragonfly-0.1.2.crate) = aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf
SIZE (rust/crates/errno-dragonfly-0.1.2.crate) = 1810
SHA256 (rust/crates/getrandom-0.2.10.crate) = be4136b2a15dd319360be1c07d9933517ccf0be8f16bf62a3bee4f0d618df427
SIZE (rust/crates/getrandom-0.2.10.crate) = 34955
SHA256 (rust/crates/hashbrown-0.12.3.crate) = 8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888
@ -39,16 +49,22 @@ SHA256 (rust/crates/heck-0.4.1.crate) = 95505c38b4572b2d910cecb0281560f54b440a19
SIZE (rust/crates/heck-0.4.1.crate) = 11567
SHA256 (rust/crates/hermit-abi-0.1.19.crate) = 62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33
SIZE (rust/crates/hermit-abi-0.1.19.crate) = 9979
SHA256 (rust/crates/hermit-abi-0.3.2.crate) = 443144c8cdadd93ebf52ddb4056d257f5b52c04d3c804e657d19eb73fc33668b
SIZE (rust/crates/hermit-abi-0.3.2.crate) = 13783
SHA256 (rust/crates/indexmap-1.9.3.crate) = bd070e393353796e801d209ad339e89596eb4c8d430d18ede6a1cced8fafbd99
SIZE (rust/crates/indexmap-1.9.3.crate) = 54653
SHA256 (rust/crates/indexmap-2.0.0.crate) = d5477fe2230a79769d8dc68e0eabf5437907c0457a5614a9e8dddb67f65eb65d
SIZE (rust/crates/indexmap-2.0.0.crate) = 64038
SHA256 (rust/crates/is-terminal-0.4.9.crate) = cb0889898416213fab133e1d33a0e5858a48177452750691bde3666d0fdbaf8b
SIZE (rust/crates/is-terminal-0.4.9.crate) = 8109
SHA256 (rust/crates/lazy_static-1.4.0.crate) = e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646
SIZE (rust/crates/lazy_static-1.4.0.crate) = 10443
SHA256 (rust/crates/libc-0.2.147.crate) = b4668fb0ea861c1df094127ac5f1da3409a82116a4ba74fca2e58ef927159bb3
SIZE (rust/crates/libc-0.2.147.crate) = 686772
SHA256 (rust/crates/libloading-0.8.0.crate) = d580318f95776505201b28cf98eb1fa5e4be3b689633ba6a3e6cd880ff22d8cb
SIZE (rust/crates/libloading-0.8.0.crate) = 27845
SHA256 (rust/crates/linux-raw-sys-0.4.5.crate) = 57bcfdad1b858c2db7c38303a6d2ad4dfaf5eb53dfeb0910128b2c26d6158503
SIZE (rust/crates/linux-raw-sys-0.4.5.crate) = 1274380
SHA256 (rust/crates/memchr-2.5.0.crate) = 2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d
SIZE (rust/crates/memchr-2.5.0.crate) = 65812
SHA256 (rust/crates/minimal-lexical-0.2.1.crate) = 68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a
@ -79,26 +95,30 @@ SHA256 (rust/crates/proc-macro-error-1.0.4.crate) = da25490ff9892aab3fcf7c36f08c
SIZE (rust/crates/proc-macro-error-1.0.4.crate) = 25293
SHA256 (rust/crates/proc-macro-error-attr-1.0.4.crate) = a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869
SIZE (rust/crates/proc-macro-error-attr-1.0.4.crate) = 7971
SHA256 (rust/crates/proc-macro2-1.0.63.crate) = 7b368fba921b0dce7e60f5e04ec15e565b3303972b42bcfde1d0713b881959eb
SIZE (rust/crates/proc-macro2-1.0.63.crate) = 44867
SHA256 (rust/crates/quote-1.0.28.crate) = 1b9ab9c7eadfd8df19006f1cf1a4aed13540ed5cbc047010ece5826e10825488
SIZE (rust/crates/quote-1.0.28.crate) = 28382
SHA256 (rust/crates/proc-macro2-1.0.66.crate) = 18fb31db3f9bddb2ea821cde30a9f70117e3f119938b5ee630b7403aa6e2ead9
SIZE (rust/crates/proc-macro2-1.0.66.crate) = 43575
SHA256 (rust/crates/quote-1.0.32.crate) = 50f3b39ccfb720540debaa0164757101c08ecb8d326b15358ce76a62c7e85965
SIZE (rust/crates/quote-1.0.32.crate) = 28037
SHA256 (rust/crates/redox_syscall-0.2.16.crate) = fb5a58c1855b4b6819d59012155603f0b22ad30cad752600aadfcb695265519a
SIZE (rust/crates/redox_syscall-0.2.16.crate) = 24012
SHA256 (rust/crates/redox_users-0.4.3.crate) = b033d837a7cf162d7993aded9304e30a83213c648b6e389db233191f891e5c2b
SIZE (rust/crates/redox_users-0.4.3.crate) = 15353
SHA256 (rust/crates/regex-1.8.4.crate) = d0ab3ca65655bb1e41f2a8c8cd662eb4fb035e67c3f78da1d61dffe89d07300f
SIZE (rust/crates/regex-1.8.4.crate) = 249562
SHA256 (rust/crates/regex-syntax-0.7.2.crate) = 436b050e76ed2903236f032a59761c1eb99e1b0aead2c257922771dab1fc8c78
SIZE (rust/crates/regex-syntax-0.7.2.crate) = 339778
SHA256 (rust/crates/rustversion-1.0.12.crate) = 4f3208ce4d8448b3f3e7d168a73f5e0c43a61e32930de3bceeccedb388b6bf06
SIZE (rust/crates/rustversion-1.0.12.crate) = 17278
SHA256 (rust/crates/regex-1.9.3.crate) = 81bc1d4caf89fac26a70747fe603c130093b53c773888797a6329091246d651a
SIZE (rust/crates/regex-1.9.3.crate) = 252676
SHA256 (rust/crates/regex-automata-0.3.6.crate) = fed1ceff11a1dddaee50c9dc8e4938bd106e9d89ae372f192311e7da498e3b69
SIZE (rust/crates/regex-automata-0.3.6.crate) = 607174
SHA256 (rust/crates/regex-syntax-0.7.4.crate) = e5ea92a5b6195c6ef2a0295ea818b312502c6fc94dde986c5553242e18fd4ce2
SIZE (rust/crates/regex-syntax-0.7.4.crate) = 343365
SHA256 (rust/crates/rustix-0.38.7.crate) = 172891ebdceb05aa0005f533a6cbfca599ddd7d966f6f5d4d9b2e70478e70399
SIZE (rust/crates/rustix-0.38.7.crate) = 332031
SHA256 (rust/crates/rustversion-1.0.14.crate) = 7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4
SIZE (rust/crates/rustversion-1.0.14.crate) = 17261
SHA256 (rust/crates/same-file-1.0.6.crate) = 93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502
SIZE (rust/crates/same-file-1.0.6.crate) = 10183
SHA256 (rust/crates/serde-1.0.164.crate) = 9e8c8cf938e98f769bc164923b06dce91cea1751522f46f8466461af04c9027d
SIZE (rust/crates/serde-1.0.164.crate) = 77057
SHA256 (rust/crates/serde_derive-1.0.164.crate) = d9735b638ccc51c28bf6914d90a2e9725b377144fc612c49a611fddd1b631d68
SIZE (rust/crates/serde_derive-1.0.164.crate) = 54789
SHA256 (rust/crates/serde-1.0.183.crate) = 32ac8da02677876d532745a130fc9d8e6edfa81a269b107c5b00829b91d8eb3c
SIZE (rust/crates/serde-1.0.183.crate) = 77210
SHA256 (rust/crates/serde_derive-1.0.183.crate) = aafe972d60b0b9bee71a91b92fee2d4fb3c9d7e8f6b179aa99f27203d99a4816
SIZE (rust/crates/serde_derive-1.0.183.crate) = 377265
SHA256 (rust/crates/serde_regex-1.1.0.crate) = a8136f1a4ea815d7eac4101cfd0b16dc0cb5e1fe1b8609dfd728058656b7badf
SIZE (rust/crates/serde_regex-1.1.0.crate) = 9710
SHA256 (rust/crates/serde_spanned-0.6.3.crate) = 96426c9936fd7a0124915f9185ea1d20aa9445cc9821142f0a73bc9207a2e186
@ -123,26 +143,26 @@ SHA256 (rust/crates/sv-parser-syntaxtree-0.13.1.crate) = 0f277d7de19e0d2acc2bf21
SIZE (rust/crates/sv-parser-syntaxtree-0.13.1.crate) = 31447
SHA256 (rust/crates/syn-1.0.109.crate) = 72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237
SIZE (rust/crates/syn-1.0.109.crate) = 237611
SHA256 (rust/crates/syn-2.0.22.crate) = 2efbeae7acf4eabd6bcdcbd11c92f45231ddda7539edc7806bd1a04a03b24616
SIZE (rust/crates/syn-2.0.22.crate) = 241001
SHA256 (rust/crates/syn-2.0.28.crate) = 04361975b3f5e348b2189d8dc55bc942f278b2d482a6a0365de5bdd62d351567
SIZE (rust/crates/syn-2.0.28.crate) = 241635
SHA256 (rust/crates/term-0.7.0.crate) = c59df8ac95d96ff9bede18eb7300b0fda5e5d8d90960e76f8e14ae765eedbf1f
SIZE (rust/crates/term-0.7.0.crate) = 37082
SHA256 (rust/crates/termcolor-1.2.0.crate) = be55cf8942feac5c765c2c993422806843c9a9a45d4d5c407ad6dd2ea95eb9b6
SIZE (rust/crates/termcolor-1.2.0.crate) = 17917
SHA256 (rust/crates/textwrap-0.16.0.crate) = 222a222a5bfe1bba4a77b45ec488a741b3cb8872e5e499451fd7d0129c9c7c3d
SIZE (rust/crates/textwrap-0.16.0.crate) = 53722
SHA256 (rust/crates/thiserror-1.0.40.crate) = 978c9a314bd8dc99be594bc3c175faaa9794be04a5a5e153caba6915336cebac
SIZE (rust/crates/thiserror-1.0.40.crate) = 18709
SHA256 (rust/crates/thiserror-impl-1.0.40.crate) = f9456a42c5b0d803c8cd86e73dd7cc9edd429499f37a3550d286d5e86720569f
SIZE (rust/crates/thiserror-impl-1.0.40.crate) = 15138
SHA256 (rust/crates/toml-0.7.5.crate) = 1ebafdf5ad1220cb59e7d17cf4d2c72015297b75b19a10472f99b89225089240
SIZE (rust/crates/toml-0.7.5.crate) = 49069
SHA256 (rust/crates/thiserror-1.0.44.crate) = 611040a08a0439f8248d1990b111c95baa9c704c805fa1f62104b39655fd7f90
SIZE (rust/crates/thiserror-1.0.44.crate) = 18760
SHA256 (rust/crates/thiserror-impl-1.0.44.crate) = 090198534930841fab3a5d1bb637cde49e339654e606195f8d9c76eeb081dc96
SIZE (rust/crates/thiserror-impl-1.0.44.crate) = 15086
SHA256 (rust/crates/toml-0.7.6.crate) = c17e963a819c331dcacd7ab957d80bc2b9a9c1e71c804826d2f283dd65306542
SIZE (rust/crates/toml-0.7.6.crate) = 49220
SHA256 (rust/crates/toml_datetime-0.6.3.crate) = 7cda73e2f1397b1262d6dfdcef8aafae14d1de7748d66822d3bfeeb6d03e5e4b
SIZE (rust/crates/toml_datetime-0.6.3.crate) = 10770
SHA256 (rust/crates/toml_edit-0.19.11.crate) = 266f016b7f039eec8a1a80dfe6156b633d208b9fccca5e4db1d6775b0c4e34a7
SIZE (rust/crates/toml_edit-0.19.11.crate) = 95642
SHA256 (rust/crates/unicode-ident-1.0.9.crate) = b15811caf2415fb889178633e7724bad2509101cde276048e013b9def5e51fa0
SIZE (rust/crates/unicode-ident-1.0.9.crate) = 41978
SHA256 (rust/crates/toml_edit-0.19.14.crate) = f8123f27e969974a3dfba720fdb560be359f57b44302d280ba72e76a74480e8a
SIZE (rust/crates/toml_edit-0.19.14.crate) = 94875
SHA256 (rust/crates/unicode-ident-1.0.11.crate) = 301abaae475aa91687eb82514b328ab47a211a533026cb25fc3e519b86adfc3c
SIZE (rust/crates/unicode-ident-1.0.11.crate) = 42067
SHA256 (rust/crates/version_check-0.9.4.crate) = 49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f
SIZE (rust/crates/version_check-0.9.4.crate) = 14895
SHA256 (rust/crates/walkdir-2.3.3.crate) = 36df944cda56c7d8d8b7496af378e6b16de9284591917d307c9b4d313c44e698
@ -159,8 +179,8 @@ SHA256 (rust/crates/winapi-x86_64-pc-windows-gnu-0.4.0.crate) = 712e227841d057c1
SIZE (rust/crates/winapi-x86_64-pc-windows-gnu-0.4.0.crate) = 2947998
SHA256 (rust/crates/windows-sys-0.48.0.crate) = 677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9
SIZE (rust/crates/windows-sys-0.48.0.crate) = 2628884
SHA256 (rust/crates/windows-targets-0.48.0.crate) = 7b1eb6f0cd7c80c79759c929114ef071b87354ce476d9d94271031c0497adfd5
SIZE (rust/crates/windows-targets-0.48.0.crate) = 7466
SHA256 (rust/crates/windows-targets-0.48.1.crate) = 05d4b17490f70499f20b9e791dcf6a299785ce8af4d709018206dc5b4953e95f
SIZE (rust/crates/windows-targets-0.48.1.crate) = 6902
SHA256 (rust/crates/windows_aarch64_gnullvm-0.48.0.crate) = 91ae572e1b79dba883e0d315474df7305d12f569b400fcf90581b06062f7e1bc
SIZE (rust/crates/windows_aarch64_gnullvm-0.48.0.crate) = 366543
SHA256 (rust/crates/windows_aarch64_msvc-0.48.0.crate) = b2ef27e0d7bdfcfc7b868b317c1d32c641a6fe4629c171b8928c7b08d98d7cf3
@ -175,7 +195,7 @@ SHA256 (rust/crates/windows_x86_64_gnullvm-0.48.0.crate) = 7896dbc1f41e08872e9d5
SIZE (rust/crates/windows_x86_64_gnullvm-0.48.0.crate) = 366536
SHA256 (rust/crates/windows_x86_64_msvc-0.48.0.crate) = 1a515f5799fe4961cb532f983ce2b23082366b898e52ffbce459c86f67c8378a
SIZE (rust/crates/windows_x86_64_msvc-0.48.0.crate) = 671422
SHA256 (rust/crates/winnow-0.4.7.crate) = ca0ace3845f0d96209f0375e6d367e3eb87eb65d27d445bdc9f1843a26f39448
SIZE (rust/crates/winnow-0.4.7.crate) = 142640
SHA256 (dalance-svlint-v0.8.0_GH0.tar.gz) = 50a5d225351ef4971d766f2c1bb80af3ae36990c6b02ae3adb4c52a26f33d82d
SIZE (dalance-svlint-v0.8.0_GH0.tar.gz) = 188243
SHA256 (rust/crates/winnow-0.5.4.crate) = acaaa1190073b2b101e15083c38ee8ec891b5e05cbee516521e94ec008f61e64
SIZE (rust/crates/winnow-0.5.4.crate) = 142308
SHA256 (dalance-svlint-v0.9.0_GH0.tar.gz) = 716accda481e1da015af5059348e3a5c6487d82e1e85cbcd5f6457f002cdbe37
SIZE (dalance-svlint-v0.9.0_GH0.tar.gz) = 193248

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