Enter the body of text here I was running Deseq2 fine on my M1 MacBook Pro. Then I did an update and Deseq2 plotPCA stopped working. The update apparently failed on mgcv. I seems this package does not compile for M1 arm processor and thus can not be used.
Here mgcv started to install!
installing the source package ‘mgcv’
trying URL 'https://cran.rstudio.com/src/contrib/mgcv_1.8-40.tar.gz'
Content type 'application/x-gzip' length 1175920 bytes (1.1 MB)
downloaded 1.1 MB
- installing source package ‘mgcv’ ... package ‘mgcv’ successfully unpacked and MD5 sums checked using staged installation ** libs
I get these errors ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0' ld: warning: ignoring file /usr/local/gfortran/lib/libgfortran.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64 ld: warning: ignoring file /usr/local/gfortran/lib/libquadmath.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-mgcv/00new/mgcv/libs
You can see it is trying to load Darwin libraries which do not exist.
Code should be placed in three backticks as shown below
# include your problematic code here with any corresponding output
# please also include the results of running the following in an R session
sessionInfo( )
> sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats4 stats graphics grDevices utils methods base
other attached packages:
[1] DESeq2_1.34.0 SummarizedExperiment_1.24.0 Biobase_2.54.0
[4] MatrixGenerics_1.6.0 matrixStats_0.61.0 GenomicRanges_1.46.1
[7] GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.4
[10] BiocGenerics_0.40.0 BiocManager_1.30.16
loaded via a namespace (and not attached):
[1] locfit_1.5-9.5 Rcpp_1.0.8.3 lattice_0.20-45 png_0.1-7
[5] Biostrings_2.62.0 assertthat_0.2.1 utf8_1.2.2 R6_2.5.1
[9] RSQLite_2.2.11 httr_1.4.2 ggplot2_3.3.5 pillar_1.7.0
[13] zlibbioc_1.40.0 rlang_1.0.2 rstudioapi_0.13 annotate_1.72.0
[17] blob_1.2.2 Matrix_1.4-1 splines_4.1.2 BiocParallel_1.28.3
[21] geneplotter_1.72.0 RCurl_1.98-1.6 bit_4.0.4 munsell_0.5.0
[25] DelayedArray_0.20.0 compiler_4.1.2 pkgconfig_2.0.3 tidyselect_1.1.2
[29] KEGGREST_1.34.0 tibble_3.1.6 GenomeInfoDbData_1.2.7 XML_3.99-0.9
[33] fansi_1.0.3 crayon_1.5.1 dplyr_1.0.8 bitops_1.0-7
[37] grid_4.1.2 xtable_1.8-4 gtable_0.3.0 lifecycle_1.0.1
[41] DBI_1.1.2 magrittr_2.0.3 datasets_4.1.2 scales_1.1.1
[45] cli_3.2.0 cachem_1.0.6 XVector_0.34.0 genefilter_1.76.0
[49] ellipsis_0.3.2 vctrs_0.4.0 generics_0.1.2 RColorBrewer_1.1-2
[53] tools_4.1.2 bit64_4.0.5 glue_1.6.2 purrr_0.3.4
[57] parallel_4.1.2 fastmap_1.1.0 survival_3.3-1 AnnotationDbi_1.56.2
[61] colorspace_2.0-3 memoise_2.0.1
Suggestions ?
