[R] install lapack for mac
Assa Yeroslaviz
frymor at gmail.com
Tue May 2 20:51:04 CEST 2017
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
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