Entering edit mode
I got the following error when I tried to install GSVA from bioconductor, could you please help?
clang: error: unsupported option '-fopenmp'
make: *** [blasctl.o] Error 1
ERROR: compilation failed for package ‘RhpcBLASctl’
The code I used to install GSVA was the following from bioconductor.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GSVA")
I then get the following
Old packages: 'RhpcBLASctl'
Update all/some/none? [a/s/n]:
a
There is a binary version available but the source version is later:
binary source needs_compilation
RhpcBLASctl 0.20-17 0.20-137 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘RhpcBLASctl’
trying URL 'https://cran.rstudio.com/src/contrib/RhpcBLASctl_0.20-137.tar.gz'
Content type 'application/x-gzip' length 40773 bytes (39 KB)
==================================================
downloaded 39 KB
* installing *source* package ‘RhpcBLASctl’ ...
** package ‘RhpcBLASctl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking sys/sysctl.h usability... yes
checking sys/sysctl.h presence... yes
checking for sys/sysctl.h... yes
checking for sysctl... yes
checking for sysctlbyname... yes
checking sys/sysinfo.h usability... no
checking sys/sysinfo.h presence... no
checking for sys/sysinfo.h... no
checking for get_nprocs... no
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c blasctl.c -o blasctl.o
clang: error: unsupported option '-fopenmp'
make: *** [blasctl.o] Error 1
ERROR: compilation failed for package ‘RhpcBLASctl’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RhpcBLASctl’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RhpcBLASctl’
The downloaded source packages are in
‘/private/var/folders/40/r15m2x5n3vj1vd599d25fp4h0000gn/T/Rtmpw2R313/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘RhpcBLASctl’ had non-zero exit status
Session info
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] splines grid parallel stats4 stats graphics grDevices utils
[9] datasets methods base
other attached packages:
[1] RColorBrewer_1.1-2 genefilter_1.68.0 mgcv_1.8-31
[4] nlme_3.1-147 garnett_0.2.12 monocle3_0.2.1
[7] DESeq2_1.26.0 monocle_2.14.0 DDRTree_0.1.5
[10] irlba_2.3.3 VGAM_1.1-3 Matrix_1.2-18
[13] pcaMethods_1.78.0 DropletUtils_1.6.1 AnnotationHub_2.18.0
[16] BiocFileCache_1.10.2 dbplyr_1.4.3 SeuratWrappers_0.1.0
[19] devtools_2.3.0 usethis_1.6.1 umap_0.2.5.0
[22] shinythemes_1.1.2 shinycssloaders_0.3 celda_1.2.4
[25] enrichR_2.1 shinyalert_1.1 GSVAdata_1.22.0
[28] hgu95a.db_3.2.3 GSEABase_1.48.0 graph_1.64.0
[31] annotate_1.64.0 XML_3.99-0.3 GSVA_1.34.0
[34] ape_5.3 ggtree_2.0.4 cluster_2.1.0
[37] colourpicker_1.0 data.table_1.12.8 plotly_4.9.2.1
[40] limma_3.42.2 ComplexHeatmap_2.2.0 shinyjs_1.1
[43] shiny_1.4.0.2 xtable_1.8-4 singleCellTK_1.6.0
[46] MAST_1.12.0 org.Hs.eg.db_3.10.0 reactome.db_1.70.0
[49] AnnotationDbi_1.48.0 breastCancerMAINZ_1.24.0 DOSE_3.12.0
[52] readr_1.3.1 clusterProfiler_3.14.3 ReactomePA_1.30.0
[55] SingleR_1.0.6 scRNAseq_2.0.2 openxlsx_4.1.5
[58] ROCR_1.0-11 KernSmooth_2.23-17 fields_10.3
[61] maps_3.3.0 spam_2.5-1 dotCall64_1.0-0
[64] DoubletFinder_2.0.3 sctransform_0.2.1 patchwork_1.0.0.9000
[67] cowplot_1.0.0 stringr_1.4.0 rgl_0.100.54
[70] scater_1.14.6 ggplot2_3.3.0 SingleCellExperiment_1.8.0
[73] SummarizedExperiment_1.16.1 DelayedArray_0.12.3 BiocParallel_1.20.1
[76] matrixStats_0.56.0 Biobase_2.46.0 GenomicRanges_1.38.0
[79] GenomeInfoDb_1.22.1 IRanges_2.20.2 S4Vectors_0.24.4
[82] BiocGenerics_0.32.0 gridExtra_2.3 dplyr_0.8.5
[85] Seurat_3.1.5
loaded via a namespace (and not attached):
[1] graphlayouts_0.7.0 pbapply_1.4-2
[3] lattice_0.20-41 haven_2.2.0
[5] vctrs_0.3.0 graphite_1.32.0
[7] fastICA_1.2-2 flowCore_1.52.1
[9] blob_1.2.1 survival_3.1-12
[11] RBGL_1.62.1 flowStats_3.44.0
[13] later_1.0.0 DBI_1.1.0
[15] R.utils_2.9.2 rappdirs_0.3.1
[17] uwot_0.1.8 dqrng_0.2.1
[19] jpeg_0.1-8.1 zlibbioc_1.32.0
[21] htmlwidgets_1.5.1 mvtnorm_1.1-0
[23] GlobalOptions_0.1.1 future_1.17.0
[25] leiden_0.3.3 DEoptimR_1.0-8
[27] tidygraph_1.2.0 Rcpp_1.0.4.6
[29] DT_0.13 promises_1.1.0
[31] pkgload_1.0.2 Hmisc_4.4-0
[33] openCyto_1.24.0 RcppParallel_5.0.1
[35] RSpectra_0.16-0 fs_1.4.1
[37] fastmatch_1.1-0 mnormt_1.5-7
[39] digest_0.6.25 png_0.1-7
[41] qlcMatrix_0.9.7 ggraph_2.0.2
[43] docopt_0.6.1 pkgconfig_2.0.3
[45] GO.db_3.10.0 CATALYST_1.10.3
[47] DelayedMatrixStats_1.8.0 ggbeeswarm_0.6.0
[49] nnls_1.4 iterators_1.0.12
[51] reticulate_1.15 circlize_0.4.9
[53] beeswarm_0.2.3 GetoptLong_0.1.8
[55] xfun_0.13 zoo_1.8-8
[57] tidyselect_1.1.0 reshape2_1.4.4
[59] purrr_0.3.4 ica_1.0-2
[61] pcaPP_1.9-73 viridisLite_0.3.0
[63] pkgbuild_1.0.8 rlang_0.4.6
[65] hexbin_1.28.1 manipulateWidget_0.10.1
[67] glue_1.4.1 europepmc_0.3
[69] labeling_0.3 httpuv_1.5.2
[71] BiocNeighbors_1.4.2 TH.data_1.0-10
[73] corpcor_1.6.9 DO.db_2.9
[75] MCMCprecision_0.4.0 webshot_0.5.2
[77] jsonlite_1.6.1 XVector_0.26.0
[79] bit_1.1-15.2 IDPmisc_1.1.20
[81] mime_0.9 stringi_1.4.6
[83] ConsensusClusterPlus_1.50.0 processx_3.4.2
[85] bitops_1.0-6 cli_2.0.2
[87] RSQLite_2.2.0 rrcov_1.5-2
[89] tidyr_1.0.3 pheatmap_1.0.12
[91] flowViz_1.50.0 rstudioapi_0.11
[93] ggcyto_1.14.1 qvalue_2.18.0
[95] locfit_1.5-9.4 ks_1.11.7
[97] listenv_0.8.0 miniUI_0.1.1.1
[99] gridGraphics_0.5-0 R.oo_1.23.0
[101] sessioninfo_1.1.1 readxl_1.3.1
[103] lifecycle_0.2.0 ExperimentHub_1.12.0
[105] munsell_0.5.0 cellranger_1.1.0
[107] R.methodsS3_1.8.0 codetools_0.2-16
[109] vipor_0.4.5 lmtest_0.9-37
[111] flowWorkspace_3.34.1 htmlTable_1.13.3
[113] triebeard_0.3.0 lsei_1.2-0.1
[115] BiocManager_1.30.10 abind_1.4-5
[117] FNN_1.1.3 farver_2.0.3
[119] RANN_2.6.1 askpass_1.1
[121] sparsesvd_0.2 RcppAnnoy_0.0.16
[123] tibble_3.0.1 ggdendro_0.1-20
[125] drc_3.0-1 future.apply_1.5.0
[127] dendextend_1.13.4 fda_5.1.4
[129] tidytree_0.3.3 ellipsis_0.3.1
[131] prettyunits_1.1.1 shinyBS_0.61
[133] ggridges_0.5.2 shinydashboard_0.7.1
[135] mclust_5.4.6 igraph_1.2.5
[137] RcppEigen_0.3.3.7.0 fgsea_1.12.0
[139] slam_0.1-47 remotes_2.1.1
[141] testthat_2.3.2 htmltools_0.4.0
[143] yaml_2.2.1 utf8_1.1.4
[145] interactiveDisplayBase_1.24.0 foreign_0.8-74
[147] withr_2.2.0 fitdistrplus_1.0-14
[149] bit64_0.9-7 multcomp_1.4-13
[151] foreach_1.5.0 robustbase_0.93-6
[153] combinat_0.0-8 GOSemSim_2.12.1
[155] rsvd_1.0.3 memoise_1.1.0
[157] forcats_0.5.0 rio_0.5.16
[159] flowClust_3.24.0 geneplotter_1.64.0
[161] callr_3.4.3 ps_1.3.3
[163] curl_4.3 fansi_0.4.1
[165] highr_0.8 urltools_1.7.3
[167] acepack_1.4.1 edgeR_3.28.1
[169] checkmate_2.0.0 desc_1.2.0
[171] npsurv_0.4-0.1 ellipse_0.4.1
[173] rjson_0.2.20 ggrepel_0.8.2
[175] clue_0.3-57 rprojroot_1.3-2
[177] tools_3.6.2 sandwich_2.5-1
[179] magrittr_1.5 RCurl_1.98-1.2
[181] car_3.0-7 ggplotify_0.0.5
[183] xml2_1.3.2 httr_1.4.1
[185] assertthat_0.2.1 Rhdf5lib_1.8.0
[187] globals_0.12.5 R6_2.4.1
[189] nnet_7.3-14 progress_1.2.2
[191] treeio_1.10.0 gtools_3.8.2
[193] shape_1.4.4 HDF5Array_1.14.4
[195] BiocVersion_3.10.1 BiocSingular_1.2.2
[197] rhdf5_2.30.1 carData_3.0-3
[199] colorspace_1.4-1 base64enc_0.1-3
[201] ncdfFlow_2.32.0 CytoML_1.12.1
[203] pillar_1.4.4 Rgraphviz_2.30.0
[205] tweenr_1.0.1 HSMMSingleCell_1.6.0
[207] rvcheck_0.1.8 GenomeInfoDbData_1.2.2
[209] plyr_1.8.6 gtable_0.3.0
[211] zip_2.0.4 knitr_1.28
[213] latticeExtra_0.6-29 fastmap_1.0.1
[215] crosstalk_1.1.0.1 doParallel_1.0.15
[217] openssl_1.4.1 scales_1.1.1
[219] backports_1.1.7 plotrix_3.7-8
[221] densityClust_0.3 enrichplot_1.6.1
[223] hms_0.5.3 ggforce_0.3.1
[225] Rtsne_0.15 polyclip_1.10-0
[227] FlowSOM_1.18.0 lazyeval_0.2.2
[229] Formula_1.2-3 tsne_0.1-3
[231] crayon_1.3.4 MASS_7.3-51.6
[233] pROC_1.16.2 viridis_0.5.1
[235] rpart_4.1-15 compiler_3.6.2
