Hey all,

I am getting an error when trying to install Rsubread on our server. Our cluster uses the module system and what's weird is that it only occurs with r_3.3.3 and installs properly with the msropen_3.3.2 version. All of my other packages are loaded with r_3.3.3 though so I want to install it with r_3.3.3. I have searched and found an old post on the support website (https://support.bioconductor.org/p/36641/) which seems similar but I can't figure out how to apply it to my case. Any ideas? 

> biocLite("Rsubread", type="source")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
Installing package(s) ‘Rsubread’
trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/Rsubread_1.24.2.tar.gz'
Content type 'unknown' length 9277377 bytes (8.8 MB)
==================================================
downloaded 8.8 MB
* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Linux.
** libs
icc -std=gnu99 -I/sw/R-3.3.3/lib64/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.24.2\"" -fpic  -g -O2 -std=c99  -c HelperFunctions.c -o HelperFunctions.o
HelperFunctions.c(822): error: incomplete type is not allowed
      struct ifreq ifr;
                   ^
HelperFunctions.c(823): error: incomplete type is not allowed
      struct ifconf ifc;
                    ^
HelperFunctions.c(835): error: incomplete type is not allowed
      const struct ifreq* const end = it + (ifc.ifc_len / sizeof(struct ifreq));
                                                                 ^
HelperFunctions.c(837): error: expression must be a pointer to a complete object type
      for (; it != end; ++it) {
                          ^
HelperFunctions.c(838): error: pointer to incomplete class type is not allowed
          strcpy(ifr.ifr_name, it->ifr_name);
                               ^
HelperFunctions.c(840): error: identifier "IFF_LOOPBACK" is undefined
              if (! (ifr.ifr_flags & IFF_LOOPBACK)) { // don't count loopback
                                     ^
HelperFunctions.c(1009): warning #266: function "strtok_r" declared implicitly
              feature_name = strtok_r(file_line,"\t",&token_temp);
                             ^
HelperFunctions.c(1009): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
              feature_name = strtok_r(file_line,"\t",&token_temp);
                                                     ^
HelperFunctions.c(1013): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
              chro_name = strtok_r(NULL,"\t", &token_temp);
                                              ^
HelperFunctions.c(1017): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
              char * start_ptr = strtok_r(NULL,"\t", &token_temp);
                                                     ^
HelperFunctions.c(1018): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
              char * end_ptr = strtok_r(NULL,"\t", &token_temp);
                                                   ^
HelperFunctions.c(1039): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
              char * strand_str = strtok_r(NULL,"\t", &token_temp);
                                                      ^
HelperFunctions.c(1048): warning #266: function "strtok_r" declared implicitly
              chro_name = strtok_r(file_line,"\t",&token_temp);
                          ^
HelperFunctions.c(1048): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
              chro_name = strtok_r(file_line,"\t",&token_temp);
                                                  ^
HelperFunctions.c(1049): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
              strtok_r(NULL,"\t", &token_temp);// source
                                  ^
HelperFunctions.c(1050): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
              char * feature_type = strtok_r(NULL,"\t", &token_temp);// feature_type
                                                        ^
HelperFunctions.c(1053): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
                  char * start_ptr = strtok_r(NULL,"\t", &token_temp);
                                                         ^
HelperFunctions.c(1054): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
                  char * end_ptr = strtok_r(NULL,"\t", &token_temp);
                                                       ^
HelperFunctions.c(1080): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
                  strtok_r(NULL,"\t", &token_temp);// score
                                      ^
HelperFunctions.c(1081): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
                  is_negative_strand = ('-' == (strtok_r(NULL,"\t", &token_temp)[0]));//strand
                                                                    ^
HelperFunctions.c(1081): error: expression must have arithmetic type
                  is_negative_strand = ('-' == (strtok_r(NULL,"\t", &token_temp)[0]));//strand
                                               ^
HelperFunctions.c(1082): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
                  strtok_r(NULL,"\t",&token_temp);    // "frame"
                                     ^
HelperFunctions.c(1083): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
                  char * extra_attrs = strtok_r(NULL,"\t",&token_temp);   // name_1 "val1"; name_2 "val2"; ...
                                                          ^
HelperFunctions.c(1134): warning #266: function "strtok_r" declared implicitly
          char * anno_chr = strtok_r(fl, ",", &sam_chr);
                            ^
HelperFunctions.c(1134): warning #167: argument of type "char **" is incompatible with parameter of type "char *"
          char * anno_chr = strtok_r(fl, ",", &sam_chr);
                                              ^
compilation aborted for HelperFunctions.c (code 2)
make: *** [HelperFunctions.o] Error 2
ERROR: compilation failed for package ‘Rsubread’
* removing ‘/gscratch/home/achits/R/x86_64-pc-linux-gnu-library/3.3/Rsubread’
* restoring previous ‘/gscratch/home/achits/R/x86_64-pc-linux-gnu-library/3.3/Rsubread’
The downloaded source packages are in
    ‘/tmp/Rtmp1Zc3Sl/downloaded_packages’
installation path not writeable, unable to update packages: boot, cluster,
  foreign, lattice, MASS, Matrix, mgcv, Rcpp, rpart, survival
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Rsubread’ had non-zero exit status
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
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_1.24.0
loaded via a namespace (and not attached):
[1] tools_3.3.3

The compilation errors are caused by the use of compiler 'icc'. Rsubread has been comprehensively tested on compiler 'gcc' but not on 'icc'.

I think you will probably have to switch to gcc for compiling Rsubread. The following page provides useful advice for how to do so:

https://stackoverflow.com/questions/1616983/building-r-packages-using-alternate-gcc