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This page was generated on 2023-10-20 09:38:05 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1102/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maftools 2.16.0  (landing page)
Anand Mayakonda
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/maftools
git_branch: RELEASE_3_17
git_last_commit: 39bddc8
git_last_commit_date: 2023-04-25 10:48:19 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

BUILD BIN results for maftools on kjohnson2


To the developers/maintainers of the maftools package:
- 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: maftools
Version: 2.16.0
Command: rm -rf maftools.buildbin-libdir && mkdir maftools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh maftools_2.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R maftools.buildbin-libdir
StartedAt: 2023-10-19 14:30:07 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 14:30:58 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 51.2 seconds
RetCode: 0
Status:   OK  
PackageFile: maftools_2.16.0.tgz
PackageFileSize: 11.41 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf maftools.buildbin-libdir && mkdir maftools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh maftools_2.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R maftools.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=maftools.buildbin-libdir maftools_2.16.0.tar.gz'
>>>>>>> 

* installing *source* package ‘maftools’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ntcounts.c -o ntcounts.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c snpcounts.c -o snpcounts.o
snpcounts.c:56:26: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  int nloci = countlines(bedfile);
                         ^~~~~~~
snpcounts.c:13:22: note: passing argument to parameter 'filename' here
int countlines(char *filename){
                     ^
snpcounts.c:56:7: warning: unused variable 'nloci' [-Wunused-variable]
  int nloci = countlines(bedfile);
      ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c somaticfreq.c -o somaticfreq.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o maftools.so ntcounts.o snpcounts.o somaticfreq.o /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/maftools.buildbin-libdir/00LOCK-maftools/00new/maftools/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 (maftools)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR maftools.buildbin-libdir/maftools/libs/maftools.so
>>>>>>> 

>>>>>>> Paths before fix:
maftools.buildbin-libdir/maftools/libs/maftools.so:
	maftools.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "maftools.buildbin-libdir/maftools/libs/maftools.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "maftools.buildbin-libdir/maftools/libs/maftools.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "maftools.buildbin-libdir/maftools/libs/maftools.so"

>>>>>>> Paths after fix:

maftools.buildbin-libdir/maftools/libs/maftools.so:
	maftools.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)