Cannot install CummeRbund on R v.3.3.0
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eihpos76mm • 0
@eihpos76mm-10962
Last seen 6.2 years ago

HI everyone,

I have been trying to install cummeRbund on R version 3.3.0 (2016-05-03), Bioconductor version 3.3 (BiocInstaller 1.22.2). I receive the following error:

.......

/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: *** [Matrix.so] Error 1
ERROR: compilation failed for package ‘Matrix’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/Matrix’
* restoring previous ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/Matrix’
* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c chol.f -o chol.o
/bin/bash: gfortran: command not found
make: *** [chol.o] Error 127
ERROR: compilation failed for package ‘nlme’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/nlme’
* restoring previous ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/nlme’
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Date.cpp -o Date.o
/bin/bash: g++: command not found
make: *** [Date.o] Error 127
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/Rcpp’
* restoring previous ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/Rcpp’
* installing *source* package ‘Rsamtools’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include" -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/XVector/include" -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/Biostrings/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include" -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/XVector/include" -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/Biostrings/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include" -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/XVector/include" -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/Biostrings/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c PileupBuffer.cpp -o PileupBuffer.o
/bin/bash: g++: command not found
make: *** [PileupBuffer.o] Error 127
ERROR: compilation failed for package ‘Rsamtools’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/Rsamtools’
* restoring previous ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/Rsamtools’
* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
checking for local ICUDT_DIR... icu55/data
checking for R_HOME... /usr/lib/R
checking for R... /usr/lib/R/bin/R
checking for R >= 3.1.0... yes
checking for cat... /bin/cat
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... g++ -E
configure: error: in `/tmp/RtmpBiizSy/R.INSTALL2070792bc593/stringi':
configure: error: C preprocessor "g++ -E" fails sanity check
See `config.log' for more details
ERROR: configuration failed for package ‘stringi’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/stringi’
* installing *source* package ‘plyr’ ...
** package ‘plyr’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/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
/bin/bash: g++: command not found
make: *** [RcppExports.o] Error 127
ERROR: compilation failed for package ‘plyr’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/plyr’
* restoring previous ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/plyr’
* installing *source* package ‘reshape2’ ...
** package ‘reshape2’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/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
/bin/bash: g++: command not found
make: *** [RcppExports.o] Error 127
ERROR: compilation failed for package ‘reshape2’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/reshape2’
* restoring previous ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/reshape2’
* installing *source* package ‘scales’ ...
** package ‘scales’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/user/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/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
/bin/bash: g++: command not found
make: *** [RcppExports.o] Error 127
ERROR: compilation failed for package ‘scales’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/scales’
* restoring previous ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/scales’
* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggplot2)
* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Hmisc.c -o Hmisc.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c cidxcn.f -o cidxcn.o
/bin/bash: gfortran: command not found
make: *** [cidxcn.o] Error 127
ERROR: compilation failed for package ‘Hmisc’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3/Hmisc’

The downloaded source packages are in
    ‘/tmp/RtmpXk4Dpx/downloaded_packages’
There were 22 warnings (use warnings() to see them)

>warnings()
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘httpuv’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘htmltools’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘shiny’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘interactiveDisplayBase’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationHub’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘ensembldb’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biovizBase’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Gviz’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘cummeRbund’ had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘plyr’ had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘quantreg’ had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Rsamtools’ had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘fastcluster’ had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Matrix’ had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘nlme’ had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Rcpp’ had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Rsamtools’ had non-zero exit status
18: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘stringi’ had non-zero exit status
19: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘plyr’ had non-zero exit status
20: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘reshape2’ had non-zero exit status
21: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘scales’ had non-zero exit status
22: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Hmisc’ had non-zero exit status

 

And  I have been try install the libcurl4-openssl-dev, also libxml2-dev, but keep getting an error.
Can anyone help me? Thank you very much.

 

cummeRbund RNA-Seq • 1.2k views
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Entering edit mode

By the way this is my

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.22.2

loaded via a namespace (and not attached):
[1] tools_3.3.0


Please help me if you know. Thank you

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Entering edit mode
@martin-morgan-1513
Last seen 15 days ago
United States

The strategy in general is to identify the first problem encountered -- biocLite("Matrix") from the output.

The initial complaints

/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: *** [Matrix.so] Error 1

look like R was configured to use 'system' versions of the lapack and blas libraries. These must have been present when R was built, but now they are not. The complain about -lgfortran and later complaints are about missing compilers gfortran and g++ are also basic R dependencies and fall into a similar situation.

It seems like your basic R installation is broken, maybe because R was installed under one configuration of your system and the configuration has now changed, or because you installed the r-base package using your package manager and so have the ability to run R but not build and install packages. How are you installing R? The easiest way is probably using your package manager

sudo apt-get install r-base-dev

as described in more (too much) detail at cran.r-project.org and navigating to 'R Binaries' and then ubuntu.

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Entering edit mode

Finally, it worked!! Huge thanks to you Mr. Martin. 

However I still cannot unsure why there was warning message when I am running R. like

> 'lib = "/usr/lib/R/site-library"' is not writable

But anyway, cummeRbund is worked.  I can continue analysis with R hopefully.

 

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0
Entering edit mode

This likely means that R is trying to update a package that was installed by a different user. From your earlier output I would guess this is the package Matrix, installed as su as part of r-base-dev. You are (correctly) running biocLite() as a regular user, so can't update those few packages that were installed as su. You could run R as su and update the Matrix package via biocLite("Matrix"), if that is the problem package, but be careful not to install additional packages as su.

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