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
That did not work unfortunately. Still got a very similar error.
I don't know what caused this problem. You tried to install Rsubread version 1.28.1 on R 3.3.3, but this version of Rsubread is released with R 3.4.3. Not sure if it is the difference in R version causing this compilation problem.
Yeah that worked. Probably a much better idea. Thanks for the input
Alex
Hello. I have encountered the same issue. I have tried the approach of using gcc to compile the package but unfortunately it doesn't work. Can you let me know how you resolved this problem please?
Many thanks,
Tom
If the issue you encountered is the same as the issue reported above, then have you checked if your Rsubread version matches the version of R?