Bioconductor installation problem
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Entering edit mode
liangc.mu • 0
@liangcmu-9405
Last seen 4.4 years ago

I encountered a problem when I installed Bioconductor in Ubuntu 14.04.  Here is the error information I have. 

Any comment or suggestion will be highly appreciated. 

> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.3.
Old packages: 'RcppArmadillo', 'mgcv'
Update all/some/none? [a/s/n]: a
trying URL 'http://cran.fhcrc.org/src/contrib/RcppArmadillo_0.6.400.2.2.tar.gz'
Content type 'application/x-gzip' length 986451 bytes (963 KB)
==================================================
downloaded 963 KB

* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
* checking LAPACK_LIBS: system LAPACK found
** libs
g++ -I/usr/share/R/include -DNDEBUG   -I"/usr/local/lib/R/site-library/Rcpp/include"  -I../inst/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/usr/local/lib/R/site-library/Rcpp/include"  -I../inst/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/usr/local/lib/R/site-library/Rcpp/include"  -I../inst/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c fastLm.cpp -o fastLm.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/usr/local/lib/R/site-library/RcppArmadillo’
* restoring previous ‘/usr/local/lib/R/site-library/RcppArmadillo’

The downloaded source packages are in
    ‘/tmp/RtmpO6UNRp/downloaded_packages’
trying URL 'http://cran.fhcrc.org/src/contrib/mgcv_1.8-10.tar.gz'
Content type 'application/x-gzip' length 802060 bytes (783 KB)
==================================================
downloaded 783 KB

* installing *source* package ‘mgcv’ ...
** package ‘mgcv’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c coxph.c -o coxph.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c discrete.c -o discrete.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c gdi.c -o gdi.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c magic.c -o magic.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c mat.c -o mat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c matrix.c -o matrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c mgcv.c -o mgcv.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c misc.c -o misc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c mvn.c -o mvn.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c qp.c -o qp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c soap.c -o soap.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c sparse-smooth.c -o sparse-smooth.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c tprs.c -o tprs.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o mgcv.so coxph.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -llapack -lblas -lgfortran -lm -lquadmath -fopenmp -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [mgcv.so] Error 1
ERROR: compilation failed for package ‘mgcv’
* removing ‘/usr/lib/R/library/mgcv’
* restoring previous ‘/usr/lib/R/library/mgcv’

The downloaded source packages are in
    ‘/tmp/RtmpO6UNRp/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘RcppArmadillo’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘mgcv’ had non-zero exit status
installation biocLite • 1.9k views
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Entering edit mode
@martin-morgan-1513
Last seen 9 weeks ago
United States

Probably you have installed R to use system lapack and blas libraries, but these are not in the ldconfig data base or have been moved since R was installed. Try

~$ R CMD config BLAS_LIBS
-L/home/mtmorgan/bin/R-devel/lib -lRblas
~$ R CMD config LAPACK_LIBS
-L/home/mtmorgan/bin/R-devel/lib -lRlapack
~$ R CMD config FLIBS
-lgfortran -lm -lquadmath

I guess they will return empty strings each time? Likewise I guess the following are empty?

~$ ldconfig -p |grep lapack
    liblapack.so.3 (libc6,x86-64) => /usr/lib/liblapack.so.3
    liblapack.so (libc6,x86-64) => /usr/lib/liblapack.so

If so, perhaps installing the 'dev' version of these libraries will work, e.g.,

~$ sudo apt-get install liblapack-dev 

and so on. If the libraries are already installed, then they can be added to ldconfig. It's not really clear how your system would get into this state, so maybe you should take the above as some hints rather than the truth. The Rcpp mailing list might also be helpful (although the problem comes up when installing Bioconductor packages, it is not really a Bioconductor issue).

 

 

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