I'm trying to install some packages which require compilation in R. I installed RTools from the website and was having the error that "RTools must be installed to build packages". I installed it again directly from Rstudio and am no longer having the same issue. However, I can't install the packages because of an error that path is not writable.
When trying to execute the command BiocManager::install("org.Rn.eg.db")
I get the following output and error message
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'org.Rn.eg.db'
installing the source package ‘org.Rn.eg.db’
trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/org.Rn.eg.db_3.13.0.tar.gz'
Content type 'application/x-gzip' length 57471764 bytes (54.8 MB)
downloaded 54.8 MB
'"C:\PROGRA~1\R\R-41~1.0/bin/x64/Rterm.exe"' is not recognized as an internal or external command,
operable program or batch file.
The downloaded source packages are in
‘##MY PATH’
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.1.0/library
packages:
affy, affyio, airway, AnnotationDbi, Biobase, BiocGenerics, BiocVersion, biomaRt, Biostrings, broom, colorspace, curl,
DelayedArray, devtools, dplyr, edgeR, EnhancedVolcano, fansi, GenomeInfoDb, GenomicRanges, gert, graph, Heatplus, IRanges,
KEGGREST, limma, marray, MatrixGenerics, mime, preprocessCore, S4Vectors, STRINGdb, SummarizedExperiment, topGO, VennDetail,
xfun, XVector, zip, zlibbioc
Old packages: 'BiocFileCache', 'BiocParallel', 'DESeq2', 'genefilter', 'glmnet', 'GSEABase', 'lme4', 'openxlsx', 'rio',
'stringi'
Update all/some/none? [a/s/n]:
n
Warning message:
In .inet_warning(msg) :
installation of package ‘org.Rn.eg.db’ had non-zero exit status
From running sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C LC_TIME=English_Canada.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] gprofiler2_0.2.0 DESeq2_1.32.0 SummarizedExperiment_1.22.0 Biobase_2.52.0
[5] MatrixGenerics_1.4.0 matrixStats_0.59.0 GenomicRanges_1.44.0 GenomeInfoDb_1.28.0
[9] IRanges_2.26.0 S4Vectors_0.30.0 BiocGenerics_0.38.0 factoextra_1.0.7
[13] dendextend_1.15.1 RColorBrewer_1.1-2 pheatmap_1.0.12 ggpubr_0.4.0
[17] ggtext_0.1.1 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.6
[21] purrr_0.3.4 readr_1.4.0 tidyr_1.1.3 tibble_3.1.2
[25] tidyverse_1.3.1 EnhancedVolcano_1.10.0 ggrepel_0.9.1 ggplot2_3.3.4
loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.2.1 lazyeval_0.2.2 splines_4.1.0 BiocParallel_1.26.0
[6] digest_0.6.27 htmltools_0.5.1.1 viridis_0.6.1 fansi_0.5.0 magrittr_2.0.1
[11] memoise_2.0.0 openxlsx_4.2.3 Biostrings_2.61.1 annotate_1.71.0 modelr_0.1.8
[16] extrafont_0.17 extrafontdb_1.0 colorspace_2.0-1 blob_1.2.1 rvest_1.0.0
[21] haven_2.4.1 xfun_0.24 crayon_1.4.1 RCurl_1.98-1.3 jsonlite_1.7.2
[26] genefilter_1.74.0 survival_3.2-11 glue_1.4.2 gtable_0.3.0 zlibbioc_1.39.0
[31] XVector_0.33.0 DelayedArray_0.19.0 proj4_1.0-10.1 car_3.0-10 Rttf2pt1_1.3.8
[36] maps_3.3.0 abind_1.4-5 scales_1.1.1 DBI_1.1.1 rstatix_0.7.0
[41] Rcpp_1.0.6 viridisLite_0.4.0 xtable_1.8-4 gridtext_0.1.4 foreign_0.8-81
[46] bit_4.0.4 htmlwidgets_1.5.3 httr_1.4.2 ellipsis_0.3.2 farver_2.1.0
[51] pkgconfig_2.0.3 XML_3.99-0.6 dbplyr_2.1.1 locfit_1.5-9.4 utf8_1.2.1
[56] labeling_0.4.2 tidyselect_1.1.1 rlang_0.4.11 AnnotationDbi_1.54.1 munsell_0.5.0
[61] cellranger_1.1.0 tools_4.1.0 cachem_1.0.5 cli_2.5.0 generics_0.1.0
[66] RSQLite_2.2.7 broom_0.7.7 fastmap_1.1.0 knitr_1.33 bit64_4.0.5
[71] fs_1.5.0 zip_2.2.0 KEGGREST_1.33.0 ash_1.0-15 ggrastr_0.2.3
[76] xml2_1.3.2 compiler_4.1.0 rstudioapi_0.13 beeswarm_0.4.0 plotly_4.9.4.1
[81] curl_4.3.1 png_0.1-7 ggsignif_0.6.2 reprex_2.0.0 geneplotter_1.71.0
[86] stringi_1.6.1 ggalt_0.4.0 lattice_0.20-44 Matrix_1.3-4 markdown_1.1
[91] vctrs_0.3.8 pillar_1.6.1 lifecycle_1.0.0 BiocManager_1.30.16 data.table_1.14.0
[96] bitops_1.0-7 R6_2.5.0 KernSmooth_2.23-20 gridExtra_2.3 rio_0.5.26
[101] vipor_0.4.5 MASS_7.3-54 assertthat_0.2.1 withr_2.4.2 GenomeInfoDbData_1.2.6
[106] hms_1.1.0 grid_4.1.0 carData_3.0-4 lubridate_1.7.10 ggbeeswarm_0.6.0
I met the exact same problem as you at the first use after installing the newest R and Rstudio. Then I just run Rstuio as Administrator and it worked. You can refer to the similar question for other solutions: https://community.rstudio.com/t/error-after-r-update-lib-c-program-files-r-r-3-5-0-library-is-not-writable/7947/2
Related
I am trying to install the trackViewer package in R, following the instructions on the Bioconductor websites https://www.bioconductor.org/packages/devel/bioc/vignettes/trackViewer/inst/doc/trackViewer.html.
https://bioconductor.org/packages/release/bioc/html/trackViewer.html
Every time I run the code
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("trackViewer")
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Gviz")
I get this error
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'Gviz'
I'm not sure how to circumvent this. I am ultimately looking to create a lollipop plot to showcase mutations in a gene of interest with annotations.
I would appreciate any help with this.
Session info:
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.0.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] Rcpp_1.0.9 GenomicRanges_1.48.0 GenomeInfoDb_1.32.3 IRanges_2.30.0
[5] S4Vectors_0.34.0 BiocGenerics_0.42.0 BiocManager_1.30.18
loaded via a namespace (and not attached):
[1] MatrixGenerics_1.8.1 Biobase_2.56.0 httr_1.4.3
[4] bit64_4.0.5 assertthat_0.2.1 BiocFileCache_2.4.0
[7] blob_1.2.3 BSgenome_1.64.0 GenomeInfoDbData_1.2.8
[10] Rsamtools_2.12.0 yaml_2.3.5 progress_1.2.2
[13] pillar_1.8.0 RSQLite_2.2.16 lattice_0.20-45
[16] glue_1.6.2 digest_0.6.29 RColorBrewer_1.1-3
[19] XVector_0.36.0 colorspace_2.0-3 htmltools_0.5.3
[22] Matrix_1.4-1 XML_3.99-0.10 pkgconfig_2.0.3
[25] biomaRt_2.52.0 zlibbioc_1.42.0 purrr_0.3.4
[28] scales_1.2.0 BiocParallel_1.30.3 tibble_3.1.8
[31] KEGGREST_1.36.3 generics_0.1.3 ellipsis_0.3.2
[34] cachem_1.0.6 SummarizedExperiment_1.26.1 GenomicFeatures_1.48.3
[37] cli_3.3.0 magrittr_2.0.3 crayon_1.5.1
[40] memoise_2.0.1 fansi_1.0.3 xml2_1.3.3
[43] tools_4.2.1 prettyunits_1.1.1 hms_1.1.1
[46] BiocIO_1.6.0 lifecycle_1.0.1 matrixStats_0.62.0
[49] stringr_1.4.0 munsell_0.5.0 DelayedArray_0.22.0
[52] AnnotationDbi_1.58.0 Biostrings_2.64.0 compiler_4.2.1
[55] rlang_1.0.4 RCurl_1.98-1.8 rstudioapi_0.13
[58] rjson_0.2.21 rappdirs_0.3.3 htmlwidgets_1.5.4
[61] bitops_1.0-7 restfulr_0.0.15 codetools_0.2-18
[64] DBI_1.1.3 curl_4.3.2 R6_2.5.1
[67] GenomicAlignments_1.32.1 dplyr_1.0.9 rtracklayer_1.56.1
[70] fastmap_1.1.0 bit_4.0.4 utf8_1.2.2
[73] filelock_1.0.2 stringi_1.7.8 parallel_4.2.1
[76] vctrs_0.4.1 png_0.1-7 dbplyr_2.2.1
[79] tidyselect_1.1.2
Here warning message suggests that latest version of the package is already installed and if you want to reinstall the package then use force=TRUE like this :
BiocManager::install("Gviz", force = TRUE)
I've been regularly loading data from my company database. Yesterday I installed R 4.1.3. Since then, the encoding of the data I load using pool is messed up. Not sure what encoding is used, but I'd need UTF-8.
I checked on my colleague's computer, who is still running R 4.1.2, and with the exact same code he doesn't have that issue. Any idea why? And possibly if I can set a global parameter for that?
My session info:
> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=English_Switzerland.1252 LC_CTYPE=English_Switzerland.1252 LC_MONETARY=English_Switzerland.1252 LC_NUMERIC=C
[5] LC_TIME=English_Switzerland.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] showtext_0.9-5 showtextdb_3.0 sysfonts_0.8.8 ggnewscale_0.4.6 scales_1.1.1 hrbrthemes_0.8.0 ggthemes_4.2.4 pool_0.1.6
[9] highcharter_0.9.4 reshape2_1.4.4 lubridate_1.8.0 zoo_1.8-9 viridis_0.6.2 viridisLite_0.4.0 forcats_0.5.1 stringr_1.4.0
[17] dplyr_1.0.8 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] httr_1.4.2 RMySQL_0.10.23 jsonlite_1.8.0 modelr_0.1.8 assertthat_0.2.1 TTR_0.24.3 cellranger_1.1.0 yaml_2.3.5
[9] gdtools_0.2.4 Rttf2pt1_1.3.10 pillar_1.7.0 backports_1.4.1 lattice_0.20-45 glue_1.6.2 rlist_0.4.6.2 extrafontdb_1.0
[17] digest_0.6.29 rvest_1.0.2 colorspace_2.0-3 htmltools_0.5.2 plyr_1.8.6 pkgconfig_2.0.3 broom_0.7.12 haven_2.4.3
[25] later_1.3.0 tzdb_0.2.0 generics_0.1.2 ellipsis_0.3.2 withr_2.5.0 cli_3.2.0 quantmod_0.4.18 magrittr_2.0.2
[33] crayon_1.5.0 readxl_1.3.1 evaluate_0.15 fs_1.5.2 fansi_1.0.2 xts_0.12.1 xml2_1.3.3 data.table_1.14.2
[41] tools_4.1.3 hms_1.1.1 lifecycle_1.0.1 munsell_0.5.0 reprex_2.0.1 compiler_4.1.3 systemfonts_1.0.4 rlang_1.0.2
[49] grid_4.1.3 rstudioapi_0.13 htmlwidgets_1.5.4 igraph_1.2.11 rmarkdown_2.13 gtable_0.3.0 DBI_1.1.2 curl_4.3.2
[57] R6_2.5.1 gridExtra_2.3 knitr_1.37 fastmap_1.1.0 extrafont_0.17 utf8_1.2.2 stringi_1.7.6 Rcpp_1.0.8.3
I'm trying to run topic models in R and calculate the best number of topics using the FindTopicsNumber function from the ldatuning package. If I run the following code on a macbook pro it fits the models but once it starts to calculate the first metric I get a fatal error and the R session is terminated. The code runs on a windows machine without problems. Does anyone know why it might not run on mac?
sessionInfo() output:
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
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] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5.4 rstudioapi_0.13 xml2_1.3.2 magrittr_2.0.1 tidyselect_1.1.0
[6] munsell_0.5.0 colorspace_2.0-0 tm_0.7-8 R6_2.5.0 rlang_0.4.8
[11] dplyr_1.0.2 tools_4.0.5 parallel_4.0.5 grid_4.0.5 gtable_0.3.0
[16] modeltools_0.2-23 ellipsis_0.3.1 tibble_3.0.4 lifecycle_0.2.0 crayon_1.3.4
[21] NLP_0.2-1 purrr_0.3.4 ggplot2_3.3.2 vctrs_0.3.5 glue_1.4.2
[26] slam_0.1-47 compiler_4.0.5 pillar_1.4.7 topicmodels_0.2-12 generics_0.1.0
[31] scales_1.1.1 stats4_4.0.5 pkgconfig_2.0.3 ldatuning_1.0.2
The error producing mac:
MacBook Pro 13-inch late 2013
macOS Catalina 10.15.7
(tried with R 4.0.3 and 4.0.5)
The working windows machine:
Dell XPS 15 9550
Windows 10.0.14393
(tried with R 4.0.4 and 4.0.5)
library(topicmodels)
data("AssociatedPress")
owl <- ldatuning::FindTopicsNumber(AssociatedPress, topics = c(1:10),
metrics = c("Griffiths2004", "CaoJuan2009",
"Arun2010", "Deveaud2014"),
method = "Gibbs", control = list(seed = 1234),
mc.cores = parallel::detectCores() - 1,
verbose = T)
Based on this github issue, and the observation that only the griffiths metric causes the failure, the problem appears to be caused by the Rmpfr package. Reinstalling the package (i.e. install.packages("Rmpfr"); library(Rmpfr)) and/or building the package from source may solve the issue. For detailed instruction on compiling R packages from source see https://stackoverflow.com/a/65334247/12957340
Edit
I was able to install and run the command above using the following steps:
Install required dependancies using homebrew:
brew install gsl
brew install gmp
brew install mpfr
Edit .R/Makevars file to include these lines (after following instructions in https://stackoverflow.com/a/65334247/12957340):
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++
CC=/usr/local/gfortran/bin/gcc
CXX=/usr/local/gfortran/bin/g++
PKG_LIBS=-L/usr/local/opt/gettext/lib
CFLAGS=-I/usr/local/opt/gsl/include -I/usr/local/opt/gmp/include -I/usr/local/opt/mpfr/include
LDFLAGS=-L/usr/local/opt/gsl/lib -L/usr/local/opt/gmp/lib -L/usr/local/opt/mpfr/lib -lgsl -lgslcblas
Install the required packages:
install.packages("topicmodels", type = "source")
install.packages("ldatuning", type = "source")
install.packages("Rmpfr")
And finally, run the example:
library(topicmodels)
library(ldatuning)
data("AssociatedPress")
owl <- ldatuning::FindTopicsNumber(AssociatedPress, topics = c(1:10),
metrics = c("Griffiths2004", "CaoJuan2009",
"Arun2010", "Deveaud2014"),
method = "Gibbs", control = list(seed = 1234),
mc.cores = parallel::detectCores() - 1,
verbose = T)
#> warning: topics count can't to be less than 2, incorrect values was removed.
#> fit models... done.
#> calculate metrics:
#> Griffiths2004... done.
#> CaoJuan2009... done.
#> Arun2010... done.
#> Deveaud2014... done.
>sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ldatuning_1.0.2 topicmodels_0.2-12
loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.2.1 Hmisc_4.5-0
[4] systemfonts_1.0.1 plyr_1.8.6 splines_4.0.3
[7] gmp_0.6-2 tfruns_1.5.0 usethis_2.0.1
[10] ggplot2_3.3.3 digest_0.6.27 htmltools_0.5.1.9000
[13] matrixcalc_1.0-3 viridis_0.5.1 fansi_0.4.2
[16] magrittr_2.0.1 checkmate_2.0.0 memoise_2.0.0
[19] tm_0.7-8 cluster_2.1.1 openxlsx_4.2.3
[22] remotes_2.2.0 readr_1.4.0 extrafont_0.17
[25] vroom_1.4.0 extrafontdb_1.0 prettyunits_1.1.1
[28] jpeg_0.1-8.1 sem_3.1-11 colorspace_2.0-1
[31] haven_2.3.1 xfun_0.22 dplyr_1.0.5
[34] jsonlite_1.7.2 callr_3.6.0 crayon_1.4.1
[37] microbenchmark_1.4-7 lme4_1.1-26 zeallot_0.1.0
[40] survival_3.2-10 zoo_1.8-9 glue_1.4.2
[43] gtable_0.3.0 mi_1.0 car_3.0-10
[46] pkgbuild_1.2.0 Rttf2pt1_1.3.8 Rmpfr_0.8-4
[49] abind_1.4-5 scales_1.1.1 DBI_1.1.1
[52] rstatix_0.7.0 Rcpp_1.0.6 viridisLite_0.4.0
[55] htmlTable_2.1.0 tmvnsim_1.0-2 reticulate_1.18
[58] foreign_0.8-81 bit_4.0.4 Formula_1.2-4
[61] stats4_4.0.3 htmlwidgets_1.5.3 RColorBrewer_1.1-2
[64] lavaan_0.6-8 modeltools_0.2-23 ellipsis_0.3.2
[67] pkgconfig_2.0.3 rJava_0.9-13 farver_2.1.0
[70] nnet_7.3-15 utf8_1.2.1 janitor_2.1.0
[73] tidyselect_1.1.0 rlang_0.4.11 munsell_0.5.0
[76] cellranger_1.1.0 tools_4.0.3 cachem_1.0.5
[79] cli_2.5.0 generics_0.1.0 devtools_2.3.2
[82] broom_0.7.5 evaluate_0.14 stringr_1.4.0
[85] fastmap_1.1.0 arm_1.11-2 yaml_2.2.1
[88] processx_3.5.0 knitr_1.31 bit64_4.0.5
[91] fs_1.5.0 zip_2.1.1 purrr_0.3.4
[94] randomForest_4.6-14 nlme_3.1-152 whisker_0.4
[97] slam_0.1-48 xml2_1.3.2 compiler_4.0.3
[100] rstudioapi_0.13 curl_4.3.1 png_0.1-7
[103] testthat_3.0.2 ggsignif_0.6.1 gt_0.2.2
[106] reprex_1.0.0 tibble_3.1.1 statmod_1.4.35
[109] pbivnorm_0.6.0 stringi_1.5.3 ps_1.6.0
[112] desc_1.3.0 gdtools_0.2.3 forcats_0.5.1
[115] hrbrthemes_0.8.0 lattice_0.20-41 Matrix_1.3-2
[118] tensorflow_2.4.0 keras_2.4.0 Amelia_1.7.6
[121] nloptr_1.2.2.2 tabulizerjars_1.0.1 vctrs_0.3.8
[124] pillar_1.6.1 lifecycle_1.0.0 BiocManager_1.30.12
[127] data.table_1.14.0 cowplot_1.1.1 R6_2.5.0
[130] latticeExtra_0.6-29 gridExtra_2.3 rio_0.5.26
[133] sessioninfo_1.1.1 boot_1.3-27 MASS_7.3-53.1
[136] assertthat_0.2.1 pkgload_1.2.0 rprojroot_2.0.2
[139] withr_2.4.2 mnormt_2.0.2 parallel_4.0.3
[142] hms_1.0.0 grid_4.0.3 rpart_4.1-15
[145] labelled_2.8.0 tidyr_1.1.3 coda_0.19-4
[148] minqa_1.2.4 rmarkdown_2.7 snakecase_0.11.0
[151] carData_3.0-4 NLP_0.2-1 snowfall_1.84-6.1
[154] lubridate_1.7.10 base64enc_0.1-3 bmem_1.8
[157] tabulizer_0.2.2
I recently installed both R and RStudio on a new computer, and wanted to create an RProject. I used to use the package renv before and it worked pretty well so far.
However, when I tried to initialize the renv library it first created all the necessary folders within the Rproject, but then suddenly gives th following error:
Fehler in data[[1]] . Indizierung ausserhalb der Grenzen
Afterwards it says: Fataler Fehler: unable to initialize the JIT
And finally produces a fatal error and collapses.
I already un- and reinstalled both R and RStudio twice, but without success.
Any ideas?
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=German_Switzerland.1252 LC_CTYPE=German_Switzerland.1252 LC_MONETARY=German_Switzerland.1252
[4] LC_NUMERIC=C LC_TIME=German_Switzerland.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 plyr_1.8.6 compiler_3.6.3 pillar_1.4.3 later_1.0.0 shinyjs_1.1
[7] tools_3.6.3 digest_0.6.25 viridisLite_0.3.0 jsonlite_1.7.0 lifecycle_0.1.0 tibble_2.1.3
[13] gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.7 shiny_1.4.0 DBI_1.1.0 rstudioapi_0.11
[19] crosstalk_1.0.0 RPostgreSQL_0.6-2 yaml_2.2.1 xfun_0.12 fastmap_1.0.1 stringr_1.4.0
[25] httr_1.4.1 dplyr_0.8.4 vctrs_0.2.3 htmlwidgets_1.5.1 DT_0.12 tidyselect_1.0.0
[31] leaflet_2.0.3 grid_3.6.3 data.table_1.12.8 glue_1.3.1 R6_2.4.1 plotly_4.9.2
[37] reshape2_1.4.3 tidyr_1.0.2 purrr_0.3.3 ggplot2_3.2.1 magrittr_1.5 shinycssloaders_0.3
[43] scales_1.1.0 promises_1.1.0 htmltools_0.5.0 assertthat_0.2.1 mime_0.9 xtable_1.8-4
[49] colorspace_1.4-1 httpuv_1.5.2 config_0.3 tinytex_0.20 stringi_1.4.6 lazyeval_0.2.2
[55] munsell_0.5.0 crayon_1.3.4 ```
I see that this question has been asked before, however none of the solutions seem to work for me.
I am trying to install mxnet on MacOS Mojave ver 10.14.3 for R. But I just can't get it to work.
I followed the installation instructions on the mxnet website and tried to build from source but to no success. Here's the error I get:
Error: package or namespace load failed for ‘mxnet’:
.onLoad failed in loadNamespace() for 'mxnet', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mxnet/libs/libmxnet.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mxnet/libs/libmxnet.so, 10): Library not loaded: /usr/local/opt/openblas/lib/libopenblasp-r0.3.1.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/mxnet/libs/libmxnet.so
Reason: image not found
I tried adding the soft link for openBlas using:
ln -sf /usr/local/opt/openblas/lib/libopenblasp-r0.3.* /usr/local/opt/openblas/lib/libopenblasp-r0.3.1.dylib
but it didn't work. When I run sessioninfo() in R, this is the output I get:
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.3
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] usethis_1.4.0 devtools_2.0.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 tidyr_0.8.1 prettyunits_1.0.2
[4] ps_1.1.0 visNetwork_2.0.5 assertthat_0.2.0
[7] rprojroot_1.3-2 digest_0.6.18 R6_2.3.0
[10] plyr_1.8.4 backports_1.1.2 ggplot2_3.0.0
[13] pillar_1.3.1 rlang_0.3.1 lazyeval_0.2.1
[16] rstudioapi_0.8 callr_3.0.0 DiagrammeR_1.0.0
[19] desc_1.2.0 downloader_0.4 readr_1.3.1
[22] stringr_1.3.1 htmlwidgets_1.3 igraph_1.2.2
[25] munsell_0.5.0 compiler_3.5.1 influenceR_0.1.0
[28] rgexf_0.15.3 pkgconfig_2.0.2 base64enc_0.1-3
[31] pkgbuild_1.0.2 htmltools_0.3.6 tidyselect_0.2.4
[34] tibble_2.0.1 gridExtra_2.3 XML_3.98-1.16
[37] viridisLite_0.3.0 crayon_1.3.4 dplyr_0.7.6
[40] withr_2.1.2 grid_3.5.1 jsonlite_1.6
[43] gtable_0.2.0 magrittr_1.5 scales_1.0.0
[46] cli_1.0.1 stringi_1.2.4 fs_1.2.6
[49] remotes_2.0.2 viridis_0.5.1 testthat_2.0.1
[52] bindrcpp_0.2.2 brew_1.0-6 RColorBrewer_1.1-2
[55] tools_3.5.1 glue_1.3.0 purrr_0.2.5
[58] hms_0.4.2 Rook_1.1-1 processx_3.2.0
[61] pkgload_1.0.2 yaml_2.2.0 colorspace_1.3-2
[64] sessioninfo_1.1.1 memoise_1.1.0 bindr_0.1.1
Any suggestions as to how I'd fix this?