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This page was generated on 2025-04-22 13:18 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 1980/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SharedObject 1.22.0  (landing page)
Jiefei Wang
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/SharedObject
git_branch: RELEASE_3_21
git_last_commit: 4beeb17
git_last_commit_date: 2025-04-15 11:49:51 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  

BUILD BIN results for SharedObject on kjohnson3

To the developers/maintainers of the SharedObject package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SharedObject.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: SharedObject
Version: 1.22.0
Command: rm -rf SharedObject.buildbin-libdir && mkdir SharedObject.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SharedObject_1.22.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SharedObject.buildbin-libdir
StartedAt: 2025-04-21 22:52:29 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 22:52:42 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 13.3 seconds
RetCode: 0
Status:   OK  
PackageFile: SharedObject_1.22.0.tgz
PackageFileSize: 1.98 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SharedObject.buildbin-libdir && mkdir SharedObject.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SharedObject_1.22.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SharedObject.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SharedObject.buildbin-libdir SharedObject_1.22.0.tar.gz'
>>>>>>> 

* installing *source* package ‘SharedObject’ ...
** this is package ‘SharedObject’ version ‘1.22.0’
** using staged installation
checking for gcc... clang -arch arm64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking for shm_open in -lrt... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c C_interface.cpp -o C_interface.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c altrep.cpp -o altrep.o
altrep.cpp:146:61: warning: format specifies type 'unsigned long long' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
                Rf_error("Something is wrong with the unit size: %llu\n", unitSize);
                                                                 ~~~~     ^~~~~~~~
                                                                 %zu
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c altrepRegistration.cpp -o altrepRegistration.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c numericAltrepOperations.cpp -o numericAltrepOperations.o
numericAltrepOperations.cpp:13:78: warning: format specifies type 'unsigned long long' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
        Rprintf(" (len=%llu, type=%d, COW=%d, SC=%d, SS=%d) shared object ID:%s\n", Rf_xlength(x), TYPEOF(x),
                       ~~~~                                                         ^~~~~~~~~~~~~
                       %td
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sharedMemory.cpp -o sharedMemory.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sharedObjectClass.cpp -o sharedObjectClass.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c stringAltrepOperations.cpp -o stringAltrepOperations.o
stringAltrepOperations.cpp:13:59: warning: format specifies type 'unsigned long long' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
    Rprintf(" (len=%llu, COW=%d) shared string object\n", Rf_xlength(x),
                   ~~~~                                   ^~~~~~~~~~~~~
                   %td
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SharedObject.so C_interface.o RcppExports.o altrep.o altrepRegistration.o numericAltrepOperations.o sharedMemory.o sharedObjectClass.o stringAltrepOperations.o utils.o -F/Library/Frameworks/R.framework/.. -framework R
mkdir -p ../inst/include&&\
	 mkdir -p ../inst/include/SharedObject&&\
	 mkdir -p ../inst/usrlib
ar -crv SharedObject.a C_interface.o RcppExports.o altrep.o altrepRegistration.o numericAltrepOperations.o sharedMemory.o sharedObjectClass.o stringAltrepOperations.o utils.o
a - C_interface.o
a - RcppExports.o
a - altrep.o
a - altrepRegistration.o
a - numericAltrepOperations.o
a - sharedMemory.o
a - sharedObjectClass.o
a - stringAltrepOperations.o
a - utils.o
cp "sharedMemory.h" "../inst/include/SharedObject/"&&\
	 cp SharedObject.a "../inst/usrlib/"
installing to /Users/biocbuild/bbs-3.21-bioc/meat/SharedObject.buildbin-libdir/00LOCK-SharedObject/00new/SharedObject/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 (SharedObject)


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

>>>>>>> Paths before fix:
SharedObject.buildbin-libdir/SharedObject/libs/SharedObject.so:
	SharedObject.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "SharedObject.buildbin-libdir/SharedObject/libs/SharedObject.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "SharedObject.buildbin-libdir/SharedObject/libs/SharedObject.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "SharedObject.buildbin-libdir/SharedObject/libs/SharedObject.so"

>>>>>>> Paths after fix:
SharedObject.buildbin-libdir/SharedObject/libs/SharedObject.so:
	SharedObject.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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)