Can't install in Mac M1
Closed this issue · 2 comments
JianGuoZhou3 commented
I used BiocManager::install("curatedMetagenomicData") to install, but there are some errors.
BiocManager::install("curatedMetagenomicData")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://ftp.fau.de/cran/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'curatedMetagenomicData'
also installing the dependencies ‘DirichletMultinomial’, ‘mia’
Package which is only available in source form, and may need
compilation of C/C++/Fortran: ‘DirichletMultinomial’
Do you want to attempt to install these from sources? (Yes/no/cancel)
installing the source packages ‘DirichletMultinomial’, ‘mia’, ‘curatedMetagenomicData’
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DirichletMultinomial_1.36.0.tar.gz'
Content type 'application/x-gzip' length 478666 bytes (467 KB)
==================================================
downloaded 467 KB
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/mia_1.2.7.tar.gz'
Content type 'application/x-gzip' length 1878862 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
trying URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/curatedMetagenomicData_3.2.3.tar.gz'
Content type 'application/x-gzip' length 1841917 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
* installing *source* package ‘DirichletMultinomial’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o
/bin/sh: gsl-config: command not found
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC -falign-functions=64 -Wall -g -O2 -c dirichlet_fit.c -o dirichlet_fit.o
/bin/sh: gsl-config: command not found
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC -falign-functions=64 -Wall -g -O2 -c dirichlet_fit_main.c -o dirichlet_fit_main.o
/bin/sh: gsl-config: command not found
dirichlet_fit_main.c:1:10: fatal error: 'gsl/gsl_rng.h' file not found
#include <gsl/gsl_rng.h>
Mac M1
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.2.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/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] paradox_0.8.0 ellipsis_0.3.2
[3] rprojroot_2.0.2 XVector_0.34.0
[5] set6_0.2.4 GenomicRanges_1.46.1
[7] fs_1.5.2 rstudioapi_0.13
[9] distr6_1.6.7 listenv_0.8.0
[11] remotes_2.4.2 mlr3tuning_0.12.1
[13] bit64_4.0.5 AnnotationDbi_1.56.2
[15] fansi_1.0.2 codetools_0.2-18
[17] splines_4.1.2 sparseMatrixStats_1.6.0
[19] cachem_1.0.6 mlr3pipelines_0.4.0
[21] pkgload_1.2.4 annotate_1.72.0
[23] png_0.1-7 graph_1.72.0
[25] HDF5Array_1.22.1 BiocManager_1.30.16
[27] compiler_4.1.2 httr_1.4.2
[29] backports_1.4.1 assertthat_0.2.1
[31] Matrix_1.4-0 fastmap_1.1.0
[33] cli_3.2.0 BiocSingular_1.10.0
[35] prettyunits_1.1.1 tools_4.1.2
[37] rsvd_1.0.5 ooplah_0.2.0
[39] glue_1.6.2 GenomeInfoDbData_1.2.7
[41] dplyr_1.0.8 mlr3_0.13.3
[43] Rcpp_1.0.8 Biobase_2.54.0
[45] vctrs_0.3.8 Biostrings_2.62.0
[47] rhdf5filters_1.6.0 preprocessCore_1.56.0
[49] DelayedMatrixStats_1.16.0 globals_0.14.0
[51] ps_1.6.0 brio_1.1.3
[53] testthat_3.1.2 beachmat_2.10.0
[55] lifecycle_1.0.1 irlba_2.3.5
[57] devtools_2.4.3 XML_3.99-0.9
[59] future_1.24.0 zlibbioc_1.40.0
[61] lgr_0.4.3 MatrixGenerics_1.6.0
[63] parallel_4.1.2 SummarizedExperiment_1.24.0
[65] rhdf5_2.38.0 SingleCellExperiment_1.16.0
[67] memoise_2.0.1 RSQLite_2.2.10
[69] GSVA_1.42.0 S4Vectors_0.32.3
[71] desc_1.4.1 ScaledMatrix_1.2.0
[73] checkmate_2.0.0 dictionar6_0.1.3
[75] palmerpenguins_0.1.0 BiocGenerics_0.40.0
[77] pkgbuild_1.3.1 BiocParallel_1.28.3
[79] GenomeInfoDb_1.30.1 rlang_1.0.2
[81] pkgconfig_2.0.3 matrixStats_0.61.0
[83] bitops_1.0-7 lattice_0.20-45
[85] purrr_0.3.4 Rhdf5lib_1.16.0
[87] bit_4.0.4 processx_3.5.2
[89] tidyselect_1.1.2 GSEABase_1.56.0
[91] parallelly_1.30.0 magrittr_2.0.2
[93] R6_2.5.1 IRanges_2.28.0
[95] generics_0.1.2 DelayedArray_0.20.0
[97] DBI_1.1.2 mlr3proba_0.4.4.9000
[99] pillar_1.7.0 param6_0.2.4
[101] withr_2.5.0 survival_3.3-1
[103] KEGGREST_1.34.0 RCurl_1.98-1.6
[105] tibble_3.1.6 crayon_1.5.0
[107] uuid_1.0-3 utf8_1.2.2
[109] usethis_2.1.5 grid_4.1.2
[111] data.table_1.14.2 blob_1.2.2
[113] callr_3.7.0 mlr3misc_0.10.0
[115] bbotk_0.5.1 digest_0.6.29
[117] xtable_1.8-4 stats4_4.1.2
[119] sessioninfo_1.2.2 mlr3extralearners_0.5.26
MacBook Pro (13-inch, M1, 2020)
lwaldron commented
R/Bioconductor support for M1 is a broader issue outside of our expertise, and this is an issue with dependencies rather than curatedMetagenomicData itself. Some people on StackExchange (e.g. https://stackoverflow.com/questions/67680663/installing-specific-r-packages-from-source-with-apple-m1-chip-causing-repository) and support.bioconductor.org (e.g. https://support.bioconductor.org/p/9138121/, https://support.bioconductor.org/p/9139482/#9139589) have posted solutions involving installing an x86 R with Rosetta until Bioconductor can offer an M1 binary repository.
lwaldron commented
One other option - the Docker-based used of cMD outlined at https://github.com/waldronlab/curatedMetagenomicAnalyses will work if you run an x86-based container (https://forums.docker.com/t/run-x86-intel-and-arm-based-images-on-apple-silicon-m1-macs/117123), and the cloud-based solution referenced there (http://app.orchestra.cancerdatasci.org/) will work without any setup or installation.