Multiple platform build/check report for BioC 3.20 - BUILD BIN results for mitoClone2 on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 mitoClone2 on kjohnson1

To the developers/maintainers of the mitoClone2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mitoClone2.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: mitoClone2

Version: 1.12.0

Command: rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mitoClone2_1.12.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mitoClone2.buildbin-libdir

StartedAt: 2025-01-01 15:31:32 -0500 (Wed, 01 Jan 2025)

EndedAt: 2025-01-01 15:32:40 -0500 (Wed, 01 Jan 2025)

EllapsedTime: 67.4 seconds

RetCode: 0

Status: OK

PackageFile: mitoClone2_1.12.0.tgz

PackageFileSize: 1.981 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mitoClone2_1.12.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mitoClone2.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=mitoClone2.buildbin-libdir mitoClone2_1.12.0.tar.gz'
>>>>>>> 

* installing *source* package ‘mitoClone2’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite
mkdir -p "/Users/biocbuild/bbs-3.20-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
cp scite "/Users/biocbuild/bbs-3.20-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
rm scite
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c bam2R_10x.cpp -o bam2R_10x.o
bam2R_10x.cpp:6:2: warning: '/*' within block comment [-Wcomment]
 /**************************************************************************************
 ^
bam2R_10x.cpp:8:1: warning: '/*' within block comment [-Wcomment]
/**********************************************************************
^
bam2R_10x.cpp:75:10: warning: unused variable 'bc_absent' [-Wunused-variable]
            int bc_absent;
                ^
bam2R_10x.cpp:53:9: warning: variable 'missingBC' set but not used [-Wunused-but-set-variable]
    int missingBC = 0;
        ^
bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable]
    hts_itr_t *iter = NULL;
               ^
bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable]
    int c = 0;
        ^
6 warnings generated.
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 mitoClone2.so bam2R_10x.o /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (mitoClone2)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so
>>>>>>> 

>>>>>>> Paths before fix:
mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so:
	mitoClone2.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)
	/usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5)
	/usr/lib/liblzma.5.dylib (compatibility version 6.0.0, current version 6.3.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/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/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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so"

>>>>>>> Paths after fix:
mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so:
	mitoClone2.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)
	/usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5)
	/usr/lib/liblzma.5.dylib (compatibility version 6.0.0, current version 6.3.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/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/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)