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BUILD BIN report for oligo on celaya2

This page was generated on 2020-01-16 13:29:43 -0500 (Thu, 16 Jan 2020).

Package 1170/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.51.2
Benilton Carvalho
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/oligo
Branch: master
Last Commit: 4baedd7
Last Changed Date: 2020-01-07 16:51:19 -0500 (Tue, 07 Jan 2020)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: oligo
Version: 1.51.2
Command: rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oligo_1.51.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R oligo.buildbin-libdir
StartedAt: 2020-01-16 11:25:35 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 11:26:30 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 55.3 seconds
RetCode: 0
Status:  OK 
PackageFile: oligo_1.51.2.tgz
PackageFileSize: 27.85 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oligo_1.51.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R oligo.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=oligo.buildbin-libdir oligo_1.51.2.tar.gz'
>>>>>>> 

* installing *source* package ‘oligo’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c DABG.c -o DABG.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c:18:17: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  while (!gzeof(file)){
                ^~~~
                *
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:1485:38: note: passing argument to parameter 'file' here
ZEXTERN int ZEXPORT gzeof OF((gzFile file));
                                     ^
ParserGzXYS.c:19:12: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
    gzgets(file, buffer, 1000);
           ^~~~
           *
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:1382:42: note: passing argument to parameter 'file' here
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
                                         ^
ParserGzXYS.c:46:6: warning: incompatible pointer types assigning to 'gzFile *' (aka 'struct gzFile_s **') from 'gzFile' (aka 'struct gzFile_s *') [-Wincompatible-pointer-types]
  fp = gzopen(currentFile, "rb");
     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~
ParserGzXYS.c:50:10: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  gzgets(fp, buffer, LINEMAX);
         ^~
         *
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:1382:42: note: passing argument to parameter 'file' here
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
                                         ^
ParserGzXYS.c:51:11: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  gzclose(fp);
          ^~
          *
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:1521:43: note: passing argument to parameter 'file' here
ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                                          ^
ParserGzXYS.c:134:6: warning: incompatible pointer types assigning to 'gzFile *' (aka 'struct gzFile_s **') from 'gzFile' (aka 'struct gzFile_s *') [-Wincompatible-pointer-types]
  fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb");
     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ParserGzXYS.c:138:11: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  gzclose(fp);
          ^~
          *
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:1521:43: note: passing argument to parameter 'file' here
ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                                          ^
7 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c ParserXYS.c -o ParserXYS.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c baseProfile.c -o baseProfile.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c basecontent.c -o basecontent.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c chipbackground.c -o chipbackground.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c mas5calls.c -o mas5calls.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c rma2.c -o rma2.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c trimmed.c -o trimmed.o
clang -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 oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/oligo.buildbin-libdir/00LOCK-oligo/00new/oligo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
Note: in method for ‘pm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition:
subset = "missing", target = "missing"
Note: in method for ‘mm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition:
subset = "missing", target = "missing"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
** testing if installed package keeps a record of temporary installation path
* DONE (oligo)


>>>>>>> 
>>>>>>> FIXING LINKS FOR oligo.buildbin-libdir/oligo/libs//oligo.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" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.5.2.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"