Question: Can't install edgeR because of compilation error: make: *** [R_add_prior_count.o] Error 1
0
gravatar for creasyt
16 months ago by
creasyt0
United States
creasyt0 wrote:

Hi,

I can't seem to install edgeR due to an odd compilation error (see below). The error appears to be something about "make: *** [R_add_prior_count.o] Error 1:

Has anyone encountered this error? Any ideas what might be missing (lib dependency)?

Thanks,

-todd

 

> biocLite("edgeR")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.1 (2017-06-30).
Installing package(s) ‘edgeR’
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/edgeR_3.20.1.tar.gz'
Content type 'application/x-gzip' length 1551888 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

* installing *source* package ‘edgeR’ ...
** libs
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c R_add_prior_count.cpp -o R_add_prior_count.o
R_add_prior_count.cpp: In function ‘SEXPREC* add_prior_count(SEXPREC*, SEXPREC*, SEXPREC*)’:
R_add_prior_count.cpp:53: error: expected initializer before ‘:’ token
R_add_prior_count.cpp:58: error: expected primary-expression before ‘if’
R_add_prior_count.cpp:58: error: expected ‘;’ before ‘if’
R_add_prior_count.cpp:58: error: expected primary-expression before ‘if’
R_add_prior_count.cpp:58: error: expected ‘)’ before ‘if’
R_add_prior_count.cpp:50: warning: unused variable ‘pptr’
utils.h: At global scope:
utils.h:64: warning: ‘LNtwo’ defined but not used
make: *** [R_add_prior_count.o] Error 1
ERROR: compilation failed for package ‘edgeR’
* removing ‘/usr/lib64/R/library/edgeR’



sessionInfo():


> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.9 (Santiago)

Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so

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] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] DESeq2_1.18.1              SummarizedExperiment_1.8.0
 [3] DelayedArray_0.4.1         matrixStats_0.52.2
 [5] Biobase_2.38.0             GenomicRanges_1.30.0
 [7] GenomeInfoDb_1.14.0        IRanges_2.12.0
 [9] S4Vectors_0.16.0           BiocGenerics_0.24.0
[11] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
 [1] genefilter_1.60.0       locfit_1.5-9.1          splines_3.4.1
 [4] lattice_0.20-35         colorspace_1.3-2        htmltools_0.3.6
 [7] base64enc_0.1-3         blob_1.1.0              survival_2.41-3
[10] XML_3.98-1.9            rlang_0.1.4             DBI_0.7
[13] foreign_0.8-69          BiocParallel_1.12.0     bit64_0.9-7
[16] RColorBrewer_1.1-2      GenomeInfoDbData_0.99.1 plyr_1.8.4
[19] stringr_1.2.0           zlibbioc_1.24.0         munsell_0.4.3
[22] gtable_0.2.0            htmlwidgets_0.9         memoise_1.1.0
[25] latticeExtra_0.6-28     knitr_1.17              geneplotter_1.56.0
[28] AnnotationDbi_1.40.0    htmlTable_1.9           Rcpp_0.12.14
[31] acepack_1.4.1           xtable_1.8-2            scales_0.5.0
[34] backports_1.1.1         checkmate_1.8.5         Hmisc_4.0-3
[37] annotate_1.56.1         XVector_0.18.0          bit_1.1-12
[40] gridExtra_2.3           ggplot2_2.2.1           digest_0.6.12
[43] stringi_1.1.6           grid_3.4.1              tools_3.4.1
[46] bitops_1.0-6            magrittr_1.5            RSQLite_2.0
[49] lazyeval_0.2.1          RCurl_1.95-4.8          tibble_1.3.4
[52] Formula_1.2-2           cluster_2.0.6           Matrix_1.2-12
[55] data.table_1.10.4-3     rpart_4.1-11            nnet_7.3-12
[58] compiler_3.4.1
edger compilation error • 991 views
ADD COMMENTlink modified 16 months ago by Gordon Smyth37k • written 16 months ago by creasyt0
Answer: Can't install edgeR because of compilation error: make: *** [R_add_prior_count.o
2
gravatar for Aaron Lun
16 months ago by
Aaron Lun23k
Cambridge, United Kingdom
Aaron Lun23k wrote:

It seems that your compiler does not have full support for the C++11 standard. This results in a failure to compile edgeR at the line in R_add_prior_count.cpp where we've used the new auto keyword. 

It seems prudent to upgrade your compiler, given that many R packages now (and probably more in the future) are taking advantage of the extra capabilities of the new standard. Admittedly, upgrading GCC usually involves yelling at your computer, your IT team, or both; but it's been 6 years, so I think we've waited long enough.

Also see some of Dirk's comments on this topic:

http://gallery.rcpp.org/articles/rcpp-and-c++11-c++14-c++17/

ADD COMMENTlink modified 16 months ago • written 16 months ago by Aaron Lun23k
Answer: Can't install edgeR because of compilation error: make: *** [R_add_prior_count.o
1
gravatar for Gordon Smyth
16 months ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

Depending on your background, it might help if I summarize Aaron's answer in simplified terms:

  1. Yes, we know this error.
  2. The error is because your Unix system is running a very old version of gcc and the current version of edgeR requires a a more recent version of gcc.
  3. If you upgrade gcc on your system (any version from the past few years will be fine, but why not the latest?), then edgeR will install fine.
ADD COMMENTlink modified 16 months ago • written 16 months ago by Gordon Smyth37k
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