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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:29:43 -0500 (Thu, 16 Jan 2020).
| Package 1170/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| oligo 1.51.2 Benilton Carvalho
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] | |
| 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 |
##############################################################################
##############################################################################
###
### 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"