[R] install lapack for mac
William Michels
wjm1 at caa.columbia.edu
Wed May 3 00:48:52 CEST 2017
Have you tried R-GUI, in the R-distribution available below?
https://cran.r-project.org/bin/macosx/
Here's a similar question on SO:
http://stackoverflow.com/questions/13476736/r-lapack-routines-cannot-be-loaded
HTH, Bill.
William Michels, Ph.D.
On Tue, May 2, 2017 at 11:51 AM, Assa Yeroslaviz <frymor at gmail.com> wrote:
> Hi,
>
> I am running R under Rstudio for the analysis of single-cell RNA-Seq data.
>
> When trying to analyse some data I keep getting the message
>
>> slicer_traj_lle <- lle(t(deng[slicer_genes,]), m = 2, k)$Y
> finding neighbours
> calculating weights
> Error in eigen(G, symmetric = TRUE, only.values = TRUE) :
> LAPACK routines cannot be loaded
>
>
> After searching the net I couldn't find a way to install LAPACK on a mac.
> When trying to install it via homebrew I get this message (this is a
> shorted message. the complete message is below):
>
> brew install lapack
>
> ...
>
> macOS already provides this software and installing another version in
>
> parallel can cause all kinds of trouble.
>
> For compilers to find this software you may need to set:
>
> LDFLAGS: -L/usr/local/opt/lapack/lib
>
> CPPFLAGS: -I/usr/local/opt/lapack/include
>
> For pkg-config to find this software you may need to set:
>
> PKG_CONFIG_PATH: /usr/local/opt/lapack/lib/pkgconfig
>
>
> I truely don't understand why my mac can't find the lapack, if it already
> there and i still can't figure out, how to tell my R tool / RStudio, where
> to find lapack.
>
> Does anyone has an idea how to do this?
>
> thanks
>
> Assa
>> R.version
> _
> platform x86_64-apple-darwin13.4.0
> arch x86_64
> os darwin13.4.0
> system x86_64, darwin13.4.0
> status
> major 3
> minor 3.1
> year 2016
> month 06
> day 21
> svn rev 70800
> language R
> version.string R version 3.3.1 (2016-06-21)
> nickname Bug in Your Hair
>
>
>> sessionInfo()
> R version 3.3.1 (2016-06-21)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.12.4 (Sierra)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] splines stats4 parallel stats graphics grDevices utils
> datasets methods
> [10] base
>
> other attached packages:
> [1] R.utils_2.5.0 R.oo_1.21.0 R.methodsS3_1.7.1
> Seurat_1.4.0.14
> [5] cowplot_0.7.0 SLICER_0.2.0 alphahull_2.1 lle_1.1
>
> [9] snowfall_1.84-6.1 snow_0.4-2 MASS_7.3-47
> scatterplot3d_0.3-40
> [13] igraph_1.0.1 destiny_2.0.8 monocle_2.2.0
> DDRTree_0.1.4
> [17] irlba_2.1.2 VGAM_1.0-3 ggplot2_2.2.1
> Biobase_2.34.0
> [21] BiocGenerics_0.20.0 Matrix_1.2-8 M3Drop_1.0.0
> numDeriv_2016.8-1
> [25] TSCAN_1.12.0
>
> loaded via a namespace (and not attached):
> [1] shinydashboard_0.5.3 lme4_1.1-13 RSQLite_1.1-2
> [4] AnnotationDbi_1.36.2 htmlwidgets_0.8 grid_3.3.1
> [7] combinat_0.0-8 trimcluster_0.1-2 ranger_0.7.0
> [10] Rtsne_0.13 munsell_0.4.3 codetools_0.2-15
> [13] statmod_1.4.29 colorspace_1.3-2 fastICA_1.2-0
> [16] knitr_1.15.1 ROCR_1.0-7 robustbase_0.92-7
> [19] vcd_1.4-3 tensor_1.5 VIM_4.7.0
> [22] TTR_0.23-1 lars_1.2 slam_0.1-40
> [25] splancs_2.01-40 bbmle_1.0.19 mnormt_1.5-5
> [28] polyclip_1.6-1 pheatmap_1.0.8 rprojroot_1.2
> [31] diptest_0.75-7 R6_2.2.0 RcppEigen_0.3.2.9.1
> [34] flexmix_2.3-14 bitops_1.0-6 spatstat.utils_1.4-1
> [37] assertthat_0.2.0 scales_0.4.1 nnet_7.3-12
> [40] gtable_0.2.0 goftest_1.1-1 MatrixModels_0.4-1
> [43] lazyeval_0.2.0 ModelMetrics_1.1.0 acepack_1.4.1
> [46] checkmate_1.8.2 reshape2_1.4.2 abind_1.4-5
> [49] backports_1.0.5 httpuv_1.3.3 rsconnect_0.7
> [52] Hmisc_4.0-2 caret_6.0-76 tools_3.3.1
> [55] gplots_3.0.1 RColorBrewer_1.1-2 proxy_0.4-16
> [58] Rcpp_0.12.10 plyr_1.8.4 base64enc_0.1-3
> [61] RCurl_1.95-4.8 rpart_4.1-11 deldir_0.1-14
> [64] pbapply_1.3-2 viridis_0.4.0 S4Vectors_0.12.2
> [67] zoo_1.8-0 cluster_2.0.6 magrittr_1.5
> [70] data.table_1.10.4 SparseM_1.77 lmtest_0.9-35
> [73] mvtnorm_1.0-6 matrixStats_0.52.2 mime_0.5
> [76] evaluate_0.10 xtable_1.8-2 smoother_1.1
> [79] pbkrtest_0.4-7 XML_3.98-1.6 mclust_5.2.3
> [82] IRanges_2.8.2 gridExtra_2.2.1 HSMMSingleCell_0.108.0
> [85] biomaRt_2.30.0 tibble_1.3.0 KernSmooth_2.23-15
> [88] minqa_1.2.4 htmltools_0.3.6 segmented_0.5-1.4
> [91] mgcv_1.8-17 Formula_1.2-1 tclust_1.2-3
> [94] DBI_0.6-1 fpc_2.1-10 boot_1.3-19
> [97] car_2.1-4 sgeostat_1.0-27 gdata_2.17.0
> [100] sn_1.5-0 foreign_0.8-68 laeken_0.4.6
> [103] sp_1.2-4 foreach_1.4.3 stringr_1.2.0
> [106] digest_0.6.12 tsne_0.1-3 rmarkdown_1.5
> [109] htmlTable_1.9 kernlab_0.9-25 shiny_1.0.3
> [112] gtools_3.5.0 quantreg_5.33 modeltools_0.2-21
> [115] nloptr_1.0.4 nlme_3.1-131 viridisLite_0.2.0
> [118] limma_3.30.13 lattice_0.20-35 DEoptimR_1.0-8
> [121] survival_2.41-3 xts_0.9-7 qlcMatrix_0.9.5
> [124] FNN_1.1 spatstat_1.50-0 prabclus_2.2-6
> [127] iterators_1.0.8 class_7.3-14 stringi_1.1.5
> [130] mixtools_1.1.0 latticeExtra_0.6-28 caTools_1.17.1
> [133] memoise_1.1.0 dplyr_0.5.0 e1071_1.6-8
> [136] ape_4.1 tripack_1.3-8
>
> ________________________
> $brew install lapack
>
> ==> *Installing dependencies for lapack: **gcc*
>
> ==> *Installing lapack dependency: **gcc*
>
> ==> *Using the sandbox*
>
> ==> *Downloading https://ftp.gnu.org/gnu/gcc/gcc-6.3.0/gcc-6.3.0.tar.bz2
> <https://ftp.gnu.org/gnu/gcc/gcc-6.3.0/gcc-6.3.0.tar.bz2>*
>
> ########################################################################
> 100.0%
>
> ==> *Downloading
> https://raw.githubusercontent.com/Homebrew/formula-patches/e9e0ee09389a54cc4c8fe1c24ebca3cd765ed0ba/gcc/6.1.0-jit.patch
> <https://raw.githubusercontent.com/Homebrew/formula-patches/e9e0ee09389a54cc4c8fe1c24ebca3cd765ed0ba/gcc/6.1.0-jit.patch>*
>
> ########################################################################
> 100.0%
>
> ==> *Patching*
>
> ==> *Applying 6.1.0-jit.patch*
>
> patching file gcc/jit/Make-lang.in
>
> ==> *../configure --build=x86_64-apple-darwin16.5.0
> --prefix=/usr/local/Cellar/gcc/6.3.0_1
> --libdir=/usr/local/Cellar/gcc/6.3.0_1/lib/gcc/6 --enable-*
>
> ==> *make bootstrap*
>
>
> ==> *make install*
>
> Error: The `brew link` step did not complete successfully
>
> The formula built, but is not symlinked into /usr/local
>
> Could not symlink bin/gfortran
>
> Target /usr/local/bin/gfortran
>
> already exists. You may want to remove it:
>
> rm '/usr/local/bin/gfortran'
>
>
> To force the link and overwrite all conflicting files:
>
> brew link --overwrite gcc
>
>
> To list all files that would be deleted:
>
> brew link --overwrite --dry-run gcc
>
>
> Possible conflicting files are:
>
> /usr/local/bin/gfortran -> /usr/local/bin/gfortran-4.8
>
> ==> *Summary*
>
> 🍺 /usr/local/Cellar/gcc/6.3.0_1: 1,358 files, 238MB, built in 120 minutes
> 1 second
>
> ==> *Installing **lapack*
>
> ==> *Downloading
> https://homebrew.bintray.com/bottles/lapack-3.7.0_2.sierra.bottle.tar.gz
> <https://homebrew.bintray.com/bottles/lapack-3.7.0_2.sierra.bottle.tar.gz>*
>
> ########################################################################
> 100.0%
>
> ==> *Pouring lapack-3.7.0_2.sierra.bottle.tar.gz*
>
> ==> *Caveats*
>
> This formula is keg-only, which means it was not symlinked into /usr/local.
>
>
> macOS already provides this software and installing another version in
>
> parallel can cause all kinds of trouble.
>
>
> For compilers to find this software you may need to set:
>
> LDFLAGS: -L/usr/local/opt/lapack/lib
>
> CPPFLAGS: -I/usr/local/opt/lapack/include
>
> For pkg-config to find this software you may need to set:
>
> PKG_CONFIG_PATH: /usr/local/opt/lapack/lib/pkgconfig
>
>
> ==> *Summary*
>
> 🍺 /usr/local/Cellar/lapack/3.7.0_2: 27 files, 10.4MB
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
More information about the R-help
mailing list