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This page was generated on 2023-10-16 11:36:59 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 566/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
distinct 1.12.2  (landing page)
Simone Tiberi
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/distinct
git_branch: RELEASE_3_17
git_last_commit: 3f26450
git_last_commit_date: 2023-05-15 05:46:56 -0400 (Mon, 15 May 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

BUILD BIN results for distinct on merida1


To the developers/maintainers of the distinct package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/distinct.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: distinct
Version: 1.12.2
Command: rm -rf distinct.buildbin-libdir && mkdir distinct.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh distinct_1.12.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R distinct.buildbin-libdir
StartedAt: 2023-10-16 09:18:07 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 09:22:39 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 272.5 seconds
RetCode: 0
Status:   OK  
PackageFile: distinct_1.12.2.tgz
PackageFileSize: 2.021 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf distinct.buildbin-libdir && mkdir distinct.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh distinct_1.12.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R distinct.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=distinct.buildbin-libdir distinct_1.12.2.tar.gz'
>>>>>>> 

* installing *source* package ‘distinct’ ...
** 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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Perm.cpp -o Perm.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Perm_covariates.cpp -o Perm_covariates.o
In file included from Perm_covariates.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/matrix.hpp:15:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:42:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:47:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val= NA_INTEGER;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:52:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val= NA_LOGICAL;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:57:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val= NA_REAL;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:62:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val = NA_STRING;
                ^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Perm_covariates_parallel.cpp -o Perm_covariates_parallel.o
In file included from Perm_covariates_parallel.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/matrix.hpp:15:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:42:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:47:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val= NA_INTEGER;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:52:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val= NA_LOGICAL;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:57:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val= NA_REAL;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:62:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val = NA_STRING;
                ^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Perm_parallel.cpp -o Perm_parallel.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o distinct.so Perm.o Perm_covariates.o Perm_covariates_parallel.o Perm_parallel.o RcppExports.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-3.17-bioc/meat/distinct.buildbin-libdir/00LOCK-distinct/00new/distinct/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 (distinct)


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

>>>>>>> Paths before fix:
distinct.buildbin-libdir/distinct/libs/distinct.so:
	distinct.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1)
	/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/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/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/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "distinct.buildbin-libdir/distinct/libs/distinct.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "distinct.buildbin-libdir/distinct/libs/distinct.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "distinct.buildbin-libdir/distinct/libs/distinct.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/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "distinct.buildbin-libdir/distinct/libs/distinct.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/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "distinct.buildbin-libdir/distinct/libs/distinct.so"

>>>>>>> Paths after fix:
distinct.buildbin-libdir/distinct/libs/distinct.so:
	distinct.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/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/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)