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 <fry...@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@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. ______________________________________________ R-help@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.