Multiple platform build/check report for BioC 3.21 - BUILD BIN results for GeneSelectMMD on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4373
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*

BUILD BIN results for GeneSelectMMD on kjohnson3

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.

raw results

Summary

Package: GeneSelectMMD

Version: 2.51.0

Command: rm -rf GeneSelectMMD.buildbin-libdir && mkdir GeneSelectMMD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeneSelectMMD_2.51.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GeneSelectMMD.buildbin-libdir

StartedAt: 2024-12-23 22:28:36 -0500 (Mon, 23 Dec 2024)

EndedAt: 2024-12-23 22:28:41 -0500 (Mon, 23 Dec 2024)

EllapsedTime: 5.1 seconds

RetCode: 0

Status: OK

PackageFile: GeneSelectMMD_2.51.0.tgz

PackageFileSize: 545.9 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GeneSelectMMD.buildbin-libdir && mkdir GeneSelectMMD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeneSelectMMD_2.51.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GeneSelectMMD.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GeneSelectMMD.buildbin-libdir GeneSelectMMD_2.51.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GeneSelectMMD’ ...
** 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) 12.2.0’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c GeneSelectMMD_init.c -o GeneSelectMMD_init.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c Qfunc.f -o Qfunc.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c blas.f -o blas.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c isnan.c -o isnan.o
/opt/gfortran/bin/gfortran -arch arm64  -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 arm64  -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 arm64  -fPIC  -Wall -g -O2  -c linpack.f -o linpack.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c llkhFun.f -o llkhFun.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c myTtest.f -o myTtest.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c paraEstLoop.f -o paraEstLoop.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pt.c -o pt.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c timer.f -o timer.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c wiFun.f -o wiFun.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 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/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-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/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/Resources/lib/libquadmath.0.dylib" "GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/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/4.5-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 4.5.0)
	/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)