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This page was generated on 2025-10-23 12:07 -0400 (Thu, 23 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4894
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4684
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4629
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 2166/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SynExtend 1.21.2  (landing page)
Nicholas Cooley
Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025)
git_url: https://git.bioconductor.org/packages/SynExtend
git_branch: devel
git_last_commit: 6662838
git_last_commit_date: 2025-10-17 08:59:08 -0400 (Fri, 17 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  

BUILD BIN results for SynExtend on kjohnson3

To the developers/maintainers of the SynExtend package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SynExtend.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: SynExtend
Version: 1.21.2
Command: rm -rf SynExtend.buildbin-libdir && mkdir SynExtend.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SynExtend_1.21.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SynExtend.buildbin-libdir
StartedAt: 2025-10-22 23:19:32 -0400 (Wed, 22 Oct 2025)
EndedAt: 2025-10-22 23:19:44 -0400 (Wed, 22 Oct 2025)
EllapsedTime: 12.3 seconds
RetCode: 0
Status:   OK  
PackageFile: SynExtend_1.21.2.tgz
PackageFileSize: 3.969 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SynExtend.buildbin-libdir && mkdir SynExtend.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SynExtend_1.21.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SynExtend.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SynExtend.buildbin-libdir SynExtend_1.21.2.tar.gz'
>>>>>>> 

* installing *source* package ‘SynExtend’ ...
** this is package ‘SynExtend’ version ‘1.21.2’
** 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 SDK: ‘MacOSX11.3.1.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c calcMIR2C.c -o calcMIR2C.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c CDend.c -o CDend.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c CShuffle.c -o CShuffle.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c dendrapply.c -o dendrapply.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c HitConsensus.c -o HitConsensus.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c HungarianAlgo.c -o HungarianAlgo.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c MoranI.c -o MoranI.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c NucleotideCounts.c -o NucleotideCounts.o
NucleotideCounts.c:267:7: warning: unused variable 'nthreads' [-Wunused-variable]
  int nthreads = INTEGER(NTHREADS)[0];
      ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_synextend.c -o R_init_synextend.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c RandomForest.c -o RandomForest.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c SEutils.c -o SEutils.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c XORRand.c -o XORRand.o
XORRand.c:67:7: warning: unused variable 'threads' [-Wunused-variable]
  int threads = INTEGER(NTHREADS)[0];
      ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c ExoLabel/ExoLabel.c -o ExoLabel/ExoLabel.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c ExoLabel/FileHandlers.c -o ExoLabel/FileHandlers.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c ExoLabel/PrefixTrie.c -o ExoLabel/PrefixTrie.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DCOMPILING_SYNEXTEND_VIA_R -fPIC  -falign-functions=64 -Wall -g -O2  -c ExoLabel/LoserTree.c -o ExoLabel/LoserTree.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c  utilfuncs.f95 -o utilfuncs.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c  tabulate_mod.f95 -o tabulate_mod.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c  cart_methods.f95 -o cart_methods.o
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SynExtend.so calcMIR2C.o CDend.o CShuffle.o dendrapply.o HitConsensus.o HungarianAlgo.o MoranI.o NucleotideCounts.o R_init_synextend.o RandomForest.o SEutils.o XORRand.o ExoLabel/ExoLabel.o ExoLabel/FileHandlers.o ExoLabel/PrefixTrie.o ExoLabel/LoserTree.o cart_methods.o tabulate_mod.o utilfuncs.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/SynExtend.buildbin-libdir/00LOCK-SynExtend/00new/SynExtend/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 (SynExtend)


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

>>>>>>> Paths before fix:
SynExtend.buildbin-libdir/SynExtend/libs/SynExtend.so:
	SynExtend.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/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" "SynExtend.buildbin-libdir/SynExtend/libs/SynExtend.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "SynExtend.buildbin-libdir/SynExtend/libs/SynExtend.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "SynExtend.buildbin-libdir/SynExtend/libs/SynExtend.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" "SynExtend.buildbin-libdir/SynExtend/libs/SynExtend.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" "SynExtend.buildbin-libdir/SynExtend/libs/SynExtend.so"

>>>>>>> Paths after fix:
SynExtend.buildbin-libdir/SynExtend/libs/SynExtend.so:
	SynExtend.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/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)