Hi all,

I'm trying to install the qvalue package on my account on the server. But, when I typed the following commands:

source('http://bioconductor.org/biocLite.R')
biocLite("qvalue")

I got the following error and warning message and the package has not been installed. However, I successfully install the "Biobase" package in the same way. Could you please help me out to solve the problem?

> source('http://bioconductor.org/biocLite.R')
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite("qvalue")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
Installing package(s) 'qvalue'
also installing the dependencies 'plyr', 'scales', 'ggplot2', 'reshape2'

trying URL 'http://cran.rstudio.com/src/contrib/plyr_1.8.4.tar.gz'
Content type 'application/x-gzip' length 392451 bytes (383 KB)
==================================================
downloaded 383 KB

trying URL 'http://cran.rstudio.com/src/contrib/scales_0.4.0.tar.gz'
Content type 'application/x-gzip' length 57358 bytes (56 KB)
==================================================
downloaded 56 KB

trying URL 'http://cran.rstudio.com/src/contrib/ggplot2_2.1.0.tar.gz'
Content type 'application/x-gzip' length 1571788 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'http://cran.rstudio.com/src/contrib/reshape2_1.4.1.tar.gz'
Content type 'application/x-gzip' length 34693 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/qvalue_2.2.2.tar.gz'
Content type 'application/x-gzip' length 2757615 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

* installing *source* package 'plyr' ...
** package 'plyr' successfully unpacked and MD5 sums checked
** libs
g++ -I/share/apps/R/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/share/apps/R/lib64/R/l                                                                        ibrary/Rcpp/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
gcc -I/share/apps/R/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/share/apps/R/lib64/R/l                                                                           ibrary/Rcpp/include"   -fpic  -g -O2  -c loop_apply.c -o loop_apply.o
loop_apply.c: In function 'loop_apply_':
loop_apply.c:15:3: error: 'for' loop initial declarations are only allowed in C99 or C11 mode
   for(int i = 0; i < n1; i++) {
   ^
loop_apply.c:15:3: note: use option -std=c99, -std=gnu99, -std=c11 or -std=gnu11 to compile y                                                                           our code
make: *** [loop_apply.o] Error 1
ERROR: compilation failed for package 'plyr'
* removing '/home/jafarinezhad/R/x86_64-pc-linux-gnu-library/3.2/plyr'
ERROR: dependency 'plyr' is not available for package 'scales'
* removing '/home/jafarinezhad/R/x86_64-pc-linux-gnu-library/3.2/scales'
ERROR: dependency 'plyr' is not available for package 'reshape2'
* removing '/home/jafarinezhad/R/x86_64-pc-linux-gnu-library/3.2/reshape2'
ERROR: dependencies 'plyr', 'reshape2', 'scales' are not available for package 'ggplot2'
* removing '/home/jafarinezhad/R/x86_64-pc-linux-gnu-library/3.2/ggplot2'
ERROR: dependencies 'ggplot2', 'reshape2' are not available for package 'qvalue'
* removing '/home/jafarinezhad/R/x86_64-pc-linux-gnu-library/3.2/qvalue'

The downloaded source packages are in
        '/tmp/Rtmptgrru9/downloaded_packages'
Old packages: 'mgcv', 'nlme', 'boot', 'cluster', 'Matrix', 'mgcv', 'nlme',
  'nnet', 'Rcpp', 'stringi', 'survival'
Update all/some/none? [a/s/n]: n
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'plyr' had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'scales' had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'reshape2' had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'ggplot2' had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'qvalue' had non-zero exit status

Also the sessionInfo() is below:

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=en_US.iso885915       LC_NAME=C
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

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

Thank you for your help in advance.

Simplify your troubleshooting by trying to install only the troublesome package

> biocLite("plyr")

Your R is configured to use the GCC C compiler in an inappropriate way. How did you install R?

$ gcc --version
gcc (Ubuntu 5.3.1-14ubuntu2.1) 5.3.1 20160413

and the flags you see are ok for that. For earlier versions of gcc it has been necessary to add -std=c99 for compilation. R should have figured this out on installation; perhaps the compiler is different from the one available when R was installed? You can work around this

$ mkdir ~/.R
$ cat > ~/.R/Makevars
CC=gcc -std=c99
^D

but it  would be better to figure out what the problem is with your R installation.