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This page was generated on 2023-04-19 11:01:54 -0400 (Wed, 19 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnsonmacOS 13.0 Venturaarm644.2.2 (2022-10-31) -- "Innocent and Trusting" 4256
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BUILD BIN results for fmcsR on kjohnson


To the developers/maintainers of the fmcsR package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 713/2183HostnameOS / ArchINSTALLBUILDBUILD BIN
fmcsR 1.40.0  (landing page)
Thomas Girke
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/fmcsR
git_branch: RELEASE_3_16
git_last_commit: 980b63e
git_last_commit_date: 2022-11-01 11:07:17 -0400 (Tue, 01 Nov 2022)
kjohnsonmacOS 13.0 Ventura / arm64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: fmcsR
Version: 1.40.0
Command: rm -rf fmcsR.buildbin-libdir && mkdir fmcsR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh fmcsR_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R fmcsR.buildbin-libdir
StartedAt: 2023-04-18 15:50:58 -0400 (Tue, 18 Apr 2023)
EndedAt: 2023-04-18 15:51:46 -0400 (Tue, 18 Apr 2023)
EllapsedTime: 48.2 seconds
RetCode: 0
Status:   OK  
PackageFile: fmcsR_1.40.0.tgz
PackageFileSize: 888.2 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf fmcsR.buildbin-libdir && mkdir fmcsR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh fmcsR_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R fmcsR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=fmcsR.buildbin-libdir fmcsR_1.40.0.tar.gz'
>>>>>>> 

* installing *source* package ‘fmcsR’ ...
** using staged installation
checking for g++... g++
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 g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for size_t... yes
checking for alarm... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating config.h
config.status: config.h is unchanged
** libs
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c MCS.cpp -o MCS.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c MCSCompound.cpp -o MCSCompound.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c MCSMap.cpp -o MCSMap.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c MCSRingDetector.cpp -o MCSRingDetector.o
MCSRingDetector.cpp:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
        int aromaticCount = 0;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
fmcs_R_wrap.cpp:47:13: warning: variable 'matchType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
            default: 
            ^~~~~~~
fmcs_R_wrap.cpp:74:13: note: uninitialized use occurs here
            matchType, runningMode, *timeout);
            ^~~~~~~~~
fmcs_R_wrap.cpp:42:6: note: variable 'matchType' is declared here
        MCS::MatchType matchType;
        ^
fmcs_R_wrap.cpp:56:13: warning: variable 'runningMode' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
            default:
            ^~~~~~~
fmcs_R_wrap.cpp:74:24: note: uninitialized use occurs here
            matchType, runningMode, *timeout);
                       ^~~~~~~~~~~
fmcs_R_wrap.cpp:52:9: note: variable 'runningMode' is declared here
        MCS::RunningMode runningMode;
        ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c util.cpp -o util.o
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o fmcsR.so MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/fmcsR.buildbin-libdir/00LOCK-fmcsR/00new/fmcsR/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 (fmcsR)


>>>>>>> 
>>>>>>> FIXING LINKS FOR fmcsR.buildbin-libdir/fmcsR/libs/fmcsR.so
>>>>>>> 

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/fmcsR.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/fmcsR.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/fmcsR.so"