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This page was generated on 2022-10-19 13:23:48 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 sSNAPPY on merida1


To the developers/maintainers of the sSNAPPY package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sSNAPPY.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 1928/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sSNAPPY 1.0.2  (landing page)
Wenjun Liu
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/sSNAPPY
git_branch: RELEASE_3_15
git_last_commit: 0e451a9
git_last_commit_date: 2022-08-02 22:40:46 -0400 (Tue, 02 Aug 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  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    OK    OK  UNNEEDED, same version is already published

Summary

Package: sSNAPPY
Version: 1.0.2
Command: rm -rf sSNAPPY.buildbin-libdir && mkdir sSNAPPY.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sSNAPPY_1.0.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sSNAPPY.buildbin-libdir
StartedAt: 2022-10-19 11:16:09 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 11:18:05 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 115.4 seconds
RetCode: 0
Status:   OK  
PackageFile: sSNAPPY_1.0.2.tgz
PackageFileSize: 1.867 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf sSNAPPY.buildbin-libdir && mkdir sSNAPPY.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sSNAPPY_1.0.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sSNAPPY.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=sSNAPPY.buildbin-libdir sSNAPPY_1.0.2.tar.gz'
>>>>>>> 

* installing *source* package ‘sSNAPPY’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c code.cpp -o code.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c normaliseByPermutation.cpp -o normaliseByPermutation.o
In file included from normaliseByPermutation.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:56:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo:22:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:333:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
  #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
          ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:338:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
    #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
            ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:341:11: warning: INFO: see the documentation for details [-W#pragma-messages]
  #pragma message ("INFO: see the documentation for details")
          ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ssPertScore.cpp -o ssPertScore.o
In file included from ssPertScore.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:56:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo:22:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:333:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
  #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
          ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:338:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
    #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
            ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:341:11: warning: INFO: see the documentation for details [-W#pragma-messages]
  #pragma message ("INFO: see the documentation for details")
          ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -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/usr/local/lib -o sSNAPPY.so RcppExports.o code.o normaliseByPermutation.o ssPertScore.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.15-bioc/meat/sSNAPPY.buildbin-libdir/00LOCK-sSNAPPY/00new/sSNAPPY/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 (sSNAPPY)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "sSNAPPY.buildbin-libdir/sSNAPPY/libs/sSNAPPY.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "sSNAPPY.buildbin-libdir/sSNAPPY/libs/sSNAPPY.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "sSNAPPY.buildbin-libdir/sSNAPPY/libs/sSNAPPY.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "sSNAPPY.buildbin-libdir/sSNAPPY/libs/sSNAPPY.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "sSNAPPY.buildbin-libdir/sSNAPPY/libs/sSNAPPY.so"