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This page was generated on 2023-02-01 11:09:10 -0500 (Wed, 01 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 epialleleR on merida1


To the developers/maintainers of the epialleleR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epialleleR.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 607/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epialleleR 1.7.0  (landing page)
Oleksii Nikolaienko
Snapshot Date: 2023-01-31 14:00:20 -0500 (Tue, 31 Jan 2023)
git_url: https://git.bioconductor.org/packages/epialleleR
git_branch: master
git_last_commit: 11ca088
git_last_commit_date: 2022-11-01 11:24:58 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: epialleleR
Version: 1.7.0
Command: rm -rf epialleleR.buildbin-libdir && mkdir epialleleR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh epialleleR_1.7.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R epialleleR.buildbin-libdir
StartedAt: 2023-02-01 08:46:50 -0500 (Wed, 01 Feb 2023)
EndedAt: 2023-02-01 08:51:25 -0500 (Wed, 01 Feb 2023)
EllapsedTime: 275.1 seconds
RetCode: 0
Status:   OK  
PackageFile: epialleleR_1.7.0.tgz
PackageFileSize: 2.373 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf epialleleR.buildbin-libdir && mkdir epialleleR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh epialleleR_1.7.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R epialleleR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=epialleleR.buildbin-libdir epialleleR_1.7.0.tar.gz'
>>>>>>> 

* installing *source* package ‘epialleleR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using C++17
using SDK: ‘’
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_cx_report.cpp -o rcpp_cx_report.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_extract_patterns.cpp -o rcpp_extract_patterns.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_fep.cpp -o rcpp_fep.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_match_target.cpp -o rcpp_match_target.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_read_bam.cpp -o rcpp_read_bam.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -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 epialleleR.so RcppExports.o rcpp_cx_report.o rcpp_extract_patterns.o rcpp_fep.o rcpp_get_base_freqs.o rcpp_get_xm_beta.o rcpp_match_target.o rcpp_read_bam.o rcpp_threshold_reads.o /Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc/meat/epialleleR.buildbin-libdir/00LOCK-epialleleR/00new/epialleleR/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 (epialleleR)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgcc_s.1.dylib" "epialleleR.buildbin-libdir/epialleleR/libs/epialleleR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgfortran.5.dylib" "epialleleR.buildbin-libdir/epialleleR/libs/epialleleR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libquadmath.0.dylib" "epialleleR.buildbin-libdir/epialleleR/libs/epialleleR.so"