BUILD BIN results for GeneSelectMMD on merida1
To the developers/maintainers of the GeneSelectMMD package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneSelectMMD.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.
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raw results
Summary
Command output
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### Running command:
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### rm -rf GeneSelectMMD.buildbin-libdir && mkdir GeneSelectMMD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeneSelectMMD_2.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GeneSelectMMD.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GeneSelectMMD.buildbin-libdir GeneSelectMMD_2.50.0.tar.gz'
>>>>>>>
* installing *source* package ‘GeneSelectMMD’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GeneSelectMMD_init.c -o GeneSelectMMD_init.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c Qfunc.f -o Qfunc.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c blas.f -o blas.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c isnan.c -o isnan.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c lbfgsb.f -o lbfgsb.o
lbfgsb.f:1409:25:
1409 | + tu,tl,wmc,wmp,wmw,ddot,tj,tj0,neggi,sbgnrm,
| ^
Warning: ‘tu’ may be used uninitialized [-Wmaybe-uninitialized]
lbfgsb.f:1482:72:
1482 | t(nbreak) = tl/(-neggi)
| ^
Warning: ‘tl’ may be used uninitialized [-Wmaybe-uninitialized]
lbfgsb.f:1409:28:
1409 | + tu,tl,wmc,wmp,wmw,ddot,tj,tj0,neggi,sbgnrm,
| ^
note: ‘tl’ was declared here
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c lbfgsbDriver.f -o lbfgsbDriver.o
lbfgsbDriver.f:243:71:
243 | + wa(2*mmax*nmax + 5*nmax + 11*mmax*mmax + 8*mmax)
| 1
Warning: Array ‘wa’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising]
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c linpack.f -o linpack.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c llkhFun.f -o llkhFun.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c myTtest.f -o myTtest.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c paraEstLoop.f -o paraEstLoop.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pt.c -o pt.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c timer.f -o timer.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c wiFun.f -o wiFun.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o GeneSelectMMD.so GeneSelectMMD_init.o Qfunc.o blas.o isnan.o lbfgsb.o lbfgsbDriver.o linpack.o llkhFun.o myTtest.o paraEstLoop.o pt.o timer.o wiFun.o -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for _lbfgsbdriver_: stack subq instruction is too different from dwarf stack size
installing to /Users/biocbuild/bbs-3.20-bioc/meat/GeneSelectMMD.buildbin-libdir/00LOCK-GeneSelectMMD/00new/GeneSelectMMD/libs
** R
** 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 (GeneSelectMMD)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so
>>>>>>>
>>>>>>> Paths before fix:
GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so:
GeneSelectMMD.so (compatibility version 0.0.0, current version 0.0.0)
/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)
/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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so"
>>>>>>> Paths after fix:
GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so:
GeneSelectMMD.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
