| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:06 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 818/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| genefilter 1.91.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
To the developers/maintainers of the genefilter package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genefilter.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: genefilter |
| Version: 1.91.0 |
| Command: rm -rf genefilter.buildbin-libdir && mkdir genefilter.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh genefilter_1.91.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R genefilter.buildbin-libdir |
| StartedAt: 2025-10-24 23:04:02 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 23:04:12 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 10.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: genefilter_1.91.0.tgz |
| PackageFileSize: 1.345 MiB |
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### Running command:
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### rm -rf genefilter.buildbin-libdir && mkdir genefilter.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh genefilter_1.91.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R genefilter.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=genefilter.buildbin-libdir genefilter_1.91.0.tar.gz'
>>>>>>>
* installing *source* package ‘genefilter’ ...
** this is package ‘genefilter’ version ‘1.91.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c half_range_mode.cpp -o half_range_mode.o
half_range_mode.cpp:100:88: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
if (diag) Rprintf( "N = %i, N'' = %i, w = %.4f, |J| = %i\n", N, N_double_prime, w, J.size() );
~~ ^~~~~~~~
%zu
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nd.c -o nd.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pAUC.c -o pAUC.o
pAUC.c:140:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if(rows != INTEGER(dimSens)[1] | columns != INTEGER(dimSens)[0])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
pAUC.c:140:8: note: cast one or both operands to int to silence this warning
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowPAUCs.c -o rowPAUCs.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowttests.c -o rowttests.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c ttest.f -o ttest.o
ttest.f:47:12:
47 | dm=dm1-dm2
| 1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:50:12:
50 | dm=dm1/dm2
| 1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:59:13:
59 | tst=(dm1-dm2)/sqrt((1.d0/ng1+1.d0/ng2)*(dss1+dss2)/(ng1+ng2-2))
| 1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:62:10:
62 | tst=(dm1-dm2)/sqrt(dss1/((ng1-1)*ng1)+dss2/((ng2-1)*ng2))
| 1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc/meat/genefilter.buildbin-libdir/00LOCK-genefilter/00new/genefilter/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 (genefilter)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR genefilter.buildbin-libdir/genefilter/libs/genefilter.so
>>>>>>>
>>>>>>> Paths before fix:
genefilter.buildbin-libdir/genefilter/libs/genefilter.so:
genefilter.so (compatibility version 0.0.0, current version 0.0.0)
/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)
/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/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "genefilter.buildbin-libdir/genefilter/libs/genefilter.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "genefilter.buildbin-libdir/genefilter/libs/genefilter.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "genefilter.buildbin-libdir/genefilter/libs/genefilter.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "genefilter.buildbin-libdir/genefilter/libs/genefilter.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "genefilter.buildbin-libdir/genefilter/libs/genefilter.so"
>>>>>>> Paths after fix:
genefilter.buildbin-libdir/genefilter/libs/genefilter.so:
genefilter.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)
/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)