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This page was generated on 2022-04-13 12:07:53 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 deepSNV on machv2


To the developers/maintainers of the deepSNV package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deepSNV.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 471/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deepSNV 1.40.0  (landing page)
Moritz Gerstung
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/deepSNV
git_branch: RELEASE_3_14
git_last_commit: 875148c
git_last_commit_date: 2021-10-26 12:01:57 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: deepSNV
Version: 1.40.0
Command: rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh deepSNV_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R deepSNV.buildbin-libdir
StartedAt: 2022-04-12 20:35:36 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 20:36:57 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 81.2 seconds
RetCode: 0
Status:   OK  
PackageFile: deepSNV_1.40.0.tgz
PackageFileSize: 3.124 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh deepSNV_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R deepSNV.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=deepSNV.buildbin-libdir deepSNV_1.40.0.tar.gz'
>>>>>>> 

* installing *source* package ‘deepSNV’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam2R.cpp -o bam2R.o
bam2R.cpp:97:13: warning: unused variable 'iter' [-Wunused-variable]
        hts_itr_t *iter = NULL;
                   ^
bam2R.cpp:100:6: warning: unused variable 'c' [-Wunused-variable]
        int c = 0;
            ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c betabinom.c -o betabinom.o
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
        int i, log=0;
               ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/usr/local/lib -o deepSNV.so bam2R.o betabinom.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.14-bioc/meat/deepSNV.buildbin-libdir/00LOCK-deepSNV/00new/deepSNV/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 (deepSNV)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "deepSNV.buildbin-libdir/deepSNV/libs/deepSNV.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "deepSNV.buildbin-libdir/deepSNV/libs/deepSNV.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "deepSNV.buildbin-libdir/deepSNV/libs/deepSNV.so"