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