Alexey Sergushichev
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/fgsea |
| git_branch: RELEASE_3_19 |
| git_last_commit: 5f63439 |
| git_last_commit_date: 2024-04-30 10:52:02 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:42 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 720/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fgsea 1.30.0 (landing page) Alexey Sergushichev
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the fgsea package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fgsea.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: fgsea |
| Version: 1.30.0 |
| Command: rm -rf fgsea.buildbin-libdir && mkdir fgsea.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh fgsea_1.30.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R fgsea.buildbin-libdir |
| StartedAt: 2024-10-18 18:29:37 -0400 (Fri, 18 Oct 2024) |
| EndedAt: 2024-10-18 18:30:22 -0400 (Fri, 18 Oct 2024) |
| EllapsedTime: 44.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: fgsea_1.30.0.tgz |
| PackageFileSize: 4.631 MiB |
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### Running command:
###
### rm -rf fgsea.buildbin-libdir && mkdir fgsea.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh fgsea_1.30.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R fgsea.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=fgsea.buildbin-libdir fgsea_1.30.0.tar.gz'
>>>>>>>
* installing *source* package ‘fgsea’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ScoreCalculation.cpp -o ScoreCalculation.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ScoreRuler.cpp -o ScoreRuler.o
In file included from ScoreRuler.cpp:2:
In file included from ./util.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c esCalculation.cpp -o esCalculation.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastGSEA.cpp -o fastGSEA.o
In file included from fastGSEA.cpp:13:
In file included from ./util.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fgseaMultilevel.cpp -o fgseaMultilevel.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
In file included from fgseaMultilevelSupplement.cpp:3:
In file included from ./util.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
^
fgseaMultilevelSupplement.cpp:77:16: warning: unused variable 'currentES' [-Wunused-variable]
double currentES = calcES(ranks, currentSamples[sampleId]);
^
fgseaMultilevelSupplement.cpp:260:14: warning: unused variable 'fl' [-Wunused-variable]
bool fl = false;
^
3 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c geseca.cpp -o geseca.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.cpp -o util.o
In file included from util.cpp:1:
In file included from ./util.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc/meat/fgsea.buildbin-libdir/00LOCK-fgsea/00new/fgsea/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fgsea)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR fgsea.buildbin-libdir/fgsea/libs/fgsea.so
>>>>>>>
>>>>>>> Paths before fix:
fgsea.buildbin-libdir/fgsea/libs/fgsea.so:
fgsea.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "fgsea.buildbin-libdir/fgsea/libs/fgsea.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "fgsea.buildbin-libdir/fgsea/libs/fgsea.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "fgsea.buildbin-libdir/fgsea/libs/fgsea.so"
>>>>>>> Paths after fix:
fgsea.buildbin-libdir/fgsea/libs/fgsea.so:
fgsea.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)