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BUILD BIN report for COMPASS on merida1

This page was generated on 2021-05-06 12:34:36 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the COMPASS package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 358/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COMPASS 1.28.0  (landing page)
Greg Finak
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/COMPASS
Branch: RELEASE_3_12
Last Commit: f1557e7
Last Changed Date: 2020-10-27 10:54:46 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: COMPASS
Version: 1.28.0
Command: rm -rf COMPASS.buildbin-libdir && mkdir COMPASS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COMPASS_1.28.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R COMPASS.buildbin-libdir
StartedAt: 2021-05-06 08:16:45 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 08:17:33 -0400 (Thu, 06 May 2021)
EllapsedTime: 48.2 seconds
RetCode: 0
Status:   OK  
PackageFile: COMPASS_1.28.0.tgz
PackageFileSize: 1.366 MiB

Command output

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###
### Running command:
###
###   rm -rf COMPASS.buildbin-libdir && mkdir COMPASS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COMPASS_1.28.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R COMPASS.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=COMPASS.buildbin-libdir COMPASS_1.28.0.tar.gz'
>>>>>>> 

* installing *source* package ‘COMPASS’ ...
** using staged installation

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source('R/cleanup.R'); cleanup()
It looks like this isn't being called from R CMD build; bailing out
> 
> 
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c COMPASS_c.c -o COMPASS_c.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c COMPASS_cpp.cpp -o COMPASS_cpp.o
In file included from COMPASS_cpp.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c COMPASS_init.c -o COMPASS_init.o
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 COMPASS.so COMPASS_c.o COMPASS_cpp.o COMPASS_init.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-3.12-bioc/meat/COMPASS.buildbin-libdir/00LOCK-COMPASS/00new/COMPASS/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (COMPASS)


>>>>>>> 
>>>>>>> FIXING LINKS FOR COMPASS.buildbin-libdir/COMPASS/libs/COMPASS.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" "COMPASS.buildbin-libdir/COMPASS/libs/COMPASS.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "COMPASS.buildbin-libdir/COMPASS/libs/COMPASS.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "COMPASS.buildbin-libdir/COMPASS/libs/COMPASS.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "COMPASS.buildbin-libdir/COMPASS/libs/COMPASS.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "COMPASS.buildbin-libdir/COMPASS/libs/COMPASS.so"