Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

BUILD BIN report for Starr on merida1

This page was generated on 2021-05-06 12:36:58 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the Starr package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1799/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Starr 1.46.0  (landing page)
Benedikt Zacher
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/Starr
Branch: RELEASE_3_12
Last Commit: f4ce49b
Last Changed Date: 2020-10-27 10:36:12 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: Starr
Version: 1.46.0
Command: rm -rf Starr.buildbin-libdir && mkdir Starr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Starr_1.46.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Starr.buildbin-libdir
StartedAt: 2021-05-06 10:08:41 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 10:09:33 -0400 (Thu, 06 May 2021)
EllapsedTime: 52.1 seconds
RetCode: 0
Status:   OK  
PackageFile: Starr_1.46.0.tgz
PackageFileSize: 1.755 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Starr.buildbin-libdir && mkdir Starr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Starr_1.46.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Starr.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Starr.buildbin-libdir Starr_1.46.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Starr’ ...
** using staged installation
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ahocorasick.c -o ahocorasick.o
ahocorasick.c:8:1: warning: unused function 'kseq_rewind' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
./kseq.h:220:2: note: expanded from macro 'KSEQ_INIT'
        __KSEQ_BASIC(type_t)                                            \
        ^
./kseq.h:152:21: note: expanded from macro '__KSEQ_BASIC'
        static inline void kseq_rewind(kseq_t *ks)                                                      \
                           ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include   -fPIC  -Wall -g -O2  -c collect.c -o collect.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rm_small_peak.c -o rm_small_peak.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sort_by_genomic.c -o sort_by_genomic.o
clang -mmacosx-version-min=10.13 -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 Starr.so ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.12-bioc/meat/Starr.buildbin-libdir/00LOCK-Starr/00new/Starr/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
Warning: Package 'Starr' is deprecated and will be removed from Bioconductor
  version 3.13
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'Starr' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (Starr)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "Starr.buildbin-libdir/Starr/libs/Starr.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "Starr.buildbin-libdir/Starr/libs/Starr.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "Starr.buildbin-libdir/Starr/libs/Starr.so"