[R] install lapack for mac
Berend Hasselman
bhh at xs4all.nl
Wed May 3 08:43:48 CEST 2017
This should have been sent to the R-SIG-Mac mailinglist.
Rstudio has nothing to do with your problem.
Which R are you using? The CRAN version?
The CRAN version has the Lapack routines included.
From which package does function lle(..) come from?
Have you tried with less packages attached?
Why homebrew? You homebrewed your R?
Please: do not post in html as the Posting guide requests.
Berend Hasselman
> On 2 May 2017, at 20:51, 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]]
>
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