[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