Hi, I am a beginner of R and Bioconductor. When I tried to install Bioconductor to my computer (OS X 10.9.5 (13F1096)) in RStudio () by
> source("http://bioconductor.org/biocLite.R")
biocLite()
Problem happened as below. How can I fix it?
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2
(2016-10-31).
Old packages: 'ade4'
Update all/some/none? [a/s/n]:
a
There is a binary version available but the source version
is later:
binary source needs_compilation
ade4 1.7-4 1.7-5 TRUE
Do you want to install from sources the package which needs compilation?
y/n: y
installing the source package ‘ade4’
trying URL 'https://cran.rstudio.com/src/contrib/ade4_1.7-5.tar.gz'
Content type 'unknown' length 3210784 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
* installing *source* package ‘ade4’ ...
** package ‘ade4’ successfully unpacked and MD5 sums checked
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c adesub.c -o adesub.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c divsub.c -o divsub.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fourthcorner.c -o fourthcorner.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c phylog.c -o phylog.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c testamova.c -o testamova.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c testdim.c -o testdim.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c testrlq.c -o testrlq.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c tests.c -o tests.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 ade4.so adesub.o divsub.o fourthcorner.o phylog.o testamova.o testdim.o testrlq.o tests.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [ade4.so] Error 1
ERROR: compilation failed for package ‘ade4’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ade4’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ade4’
The downloaded source packages are in
‘/private/var/folders/j7/l9jj2xw50zvfs1g_m9vlvwbh0000gn/T/RtmpXvgFy0/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘ade4’ had non-zero exit status
