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This page was generated on 2024-12-17 11:42 -0500 (Tue, 17 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4752
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4466
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4420
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4375
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 893/2273HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graper 1.23.0  (landing page)
Britta Velten
Snapshot Date: 2024-12-16 13:40 -0500 (Mon, 16 Dec 2024)
git_url: https://git.bioconductor.org/packages/graper
git_branch: devel
git_last_commit: 91803f0
git_last_commit_date: 2024-10-29 10:33:50 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

BUILD BIN results for graper on lconway

To the developers/maintainers of the graper package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.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: graper
Version: 1.23.0
Command: rm -rf graper.buildbin-libdir && mkdir graper.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh graper_1.23.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R graper.buildbin-libdir
StartedAt: 2024-12-17 01:04:37 -0500 (Tue, 17 Dec 2024)
EndedAt: 2024-12-17 01:05:20 -0500 (Tue, 17 Dec 2024)
EllapsedTime: 43.5 seconds
RetCode: 0
Status:   OK  
PackageFile: graper_1.23.0.tgz
PackageFileSize: 1.151 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf graper.buildbin-libdir && mkdir graper.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh graper_1.23.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R graper.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=graper.buildbin-libdir graper_1.23.0.tar.gz'
>>>>>>> 

* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c fit_graper.cpp -o fit_graper.o
In file included from fit_graper.cpp:4:
In file included from ./graper_linear_dense_ff.h:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
#    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
     ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/graper.buildbin-libdir/00LOCK-graper/00new/graper/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 (graper)


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

>>>>>>> Paths before fix:
graper.buildbin-libdir/graper/libs/graper.so:
	graper.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/x86_64-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-x86_64/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/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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "graper.buildbin-libdir/graper/libs/graper.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "graper.buildbin-libdir/graper/libs/graper.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "graper.buildbin-libdir/graper/libs/graper.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "graper.buildbin-libdir/graper/libs/graper.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "graper.buildbin-libdir/graper/libs/graper.so"

>>>>>>> Paths after fix:
graper.buildbin-libdir/graper/libs/graper.so:
	graper.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/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/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)