| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 1376/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| multtest 2.62.0 (landing page) Katherine S. Pollard
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | 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 multtest package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/multtest.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: multtest |
| Version: 2.62.0 |
| Command: rm -rf multtest.buildbin-libdir && mkdir multtest.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh multtest_2.62.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R multtest.buildbin-libdir |
| StartedAt: 2024-12-21 15:45:15 -0500 (Sat, 21 Dec 2024) |
| EndedAt: 2024-12-21 15:45:32 -0500 (Sat, 21 Dec 2024) |
| EllapsedTime: 16.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: multtest_2.62.0.tgz |
| PackageFileSize: 826.2 KiB |
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### Running command:
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### rm -rf multtest.buildbin-libdir && mkdir multtest.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh multtest_2.62.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R multtest.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=multtest.buildbin-libdir multtest_2.62.0.tar.gz'
>>>>>>>
* installing *source* package ‘multtest’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c Rpack.c -o Rpack.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c VScount.c -o VScount.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c block_sampling_fixed.c -o block_sampling_fixed.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c bootloop.c -o bootloop.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c mt.c -o mt.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c pairt_sampling.c -o pairt_sampling.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c random.c -o random.o
random.c:48:6: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
z1=abs(seed); /*setting the seed to z1 and initialize it*/
^
random.c:48:6: note: use function 'labs' instead
z1=abs(seed); /*setting the seed to z1 and initialize it*/
^~~
labs
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c sampling.c -o sampling.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c sampling_fixed.c -o sampling_fixed.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c stat_func.c -o stat_func.o
stat_func.c:185:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count=0;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c stat_order.c -o stat_order.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o multtest.so Rpack.o VScount.o block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o stat_order.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/multtest.buildbin-libdir/00LOCK-multtest/00new/multtest/libs
** R
** data
** 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 (multtest)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR multtest.buildbin-libdir/multtest/libs/multtest.so
>>>>>>>
>>>>>>> Paths before fix:
multtest.buildbin-libdir/multtest/libs/multtest.so:
multtest.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
>>>>>>> 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" "multtest.buildbin-libdir/multtest/libs/multtest.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "multtest.buildbin-libdir/multtest/libs/multtest.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "multtest.buildbin-libdir/multtest/libs/multtest.so"
>>>>>>> Paths after fix:
multtest.buildbin-libdir/multtest/libs/multtest.so:
multtest.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)