installing error for oligo package
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@jolin0701-dy-9983
Last seen 8.1 years ago

R version is 3.2.1

Mac OS X is 10.8.5.

I'd like to install oligo package and got this error.

Any help will be appreciated.

> biocLite("oligo")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.1 (2015-06-18).
Installing package(s) ‘oligo’

  There is a binary version available but the source version is later:
      binary source needs_compilation
oligo 1.34.0 1.34.2             FALSE

installing the source package ‘oligo’

trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/oligo_1.34.2.tar.gz'
Content type 'application/x-gzip' length 28420614 bytes (27.1 MB)
==================================================
downloaded 27.1 MB

* installing *source* package ‘oligo’ ...
** libs
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c DABG.c -o DABG.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c ParserGzXYS.c -o ParserGzXYS.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c ParserXYS.c -o ParserXYS.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c baseProfile.c -o baseProfile.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c basecontent.c -o basecontent.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c chipbackground.c -o chipbackground.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c mas5calls.c -o mas5calls.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c rma2.c -o rma2.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c rma_common.c -o rma_common.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c trimmed.c -o trimmed.o
gcc -arch x86_64 -std=gnu99 -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 -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/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -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
ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3'
ld: library not found for -lgfortran
collect2: ld returned 1 exit status
make: *** [oligo.so] Error 1
ERROR: compilation failed for package ‘oligo’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/oligo’

The downloaded source packages are in
    ‘/private/var/folders/cy/fksqlcls08g7fd5j971x9gs80000gp/T/RtmpE03AiY/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘oligo’ had non-zero exit status

oligo • 1.4k views
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@benilton-carvalho-1375
Last seen 4.1 years ago
Brazil/Campinas/UNICAMP
The error says you're missing a Fortran compiler on your system. 
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I installed it and it works.

Thanks so much~

 

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