Dear conductors,

I am trying to install the "affy" package. However, it has not worked despite trying multiple ways of installing. When I enter

> if (!require("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> 
> BiocManager::install("affy")

.. the output is ..

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Old packages: 'nlme'
Update all/some/none? [a/s/n]: 
a
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'

  There is a binary version available but the source version is later:
      binary  source needs_compilation
nlme 3.1-159 3.1-160              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘nlme’

trying URL 'http://cran.rstudio.com/src/contrib/nlme_3.1-160.tar.gz'
Content type 'application/x-gzip' length 845714 bytes (825 KB)
==================================================
downloaded 825 KB

* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c chol.f -o chol.o
make: /opt/R/arm64/bin/gfortran: No such file or directory
make: *** [chol.o] Error 1
ERROR: compilation failed for package ‘nlme’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/nlme’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/nlme’

The downloaded source packages are in
    ‘/private/var/folders/d5/43pf7c_937s_23qqt7xvnkd40000gp/T/RtmpDh13j4/downloaded_packages’
Warning messages:
1: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'affy' 
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘nlme’ had non-zero exit status

So there seems to be a problem with the nlme package. I uninstalled and tried re-installing 'nlme', but now it shows:

> install.packages("nlme")

  There is a binary version available but the source version is later:
      binary  source needs_compilation
nlme 3.1-159 3.1-160              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘nlme’

trying URL 'http://cran.rstudio.com/src/contrib/nlme_3.1-160.tar.gz'
Content type 'application/x-gzip' length 845714 bytes (825 KB)
==================================================
downloaded 825 KB

* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c chol.f -o chol.o
make: /opt/R/arm64/bin/gfortran: No such file or directory
make: *** [chol.o] Error 1
ERROR: compilation failed for package ‘nlme’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/nlme’
Warning in install.packages :
  installation of package ‘nlme’ had non-zero exit status

Can anyone help me figure out how to install the affy package? I seem to be needing 'nlme' which does not install and 'preprocessCore' which also gives an error message when I try to install it. Thanks in advance!

Best regards, Philipp

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-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] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] EnhancedVolcano_1.14.0 limma_3.52.4           mclust_5.4.10          ggrepel_0.9.1          hgu133plus2.db_3.13.0 
 [6] org.Hs.eg.db_3.15.0    AnnotationDbi_1.58.0   IRanges_2.30.1         S4Vectors_0.34.0       Biobase_2.56.0        
[11] BiocGenerics_0.42.0    forcats_0.5.2          stringr_1.4.1          dplyr_1.0.10           purrr_0.3.5           
[16] readr_2.1.3            tidyr_1.2.1            tibble_3.1.8           tidyverse_1.3.2        reshape2_1.4.4        
[21] fgsea_1.22.0           cowplot_1.1.1          plotly_4.10.0          ggplot2_3.3.6          readxl_1.4.1          
[26] pheatmap_1.0.12        BiocManager_1.30.18   

loaded via a namespace (and not attached):
  [1] backports_1.4.1        fastmatch_1.1-3        plyr_1.8.7             igraph_1.3.5           lazyeval_0.2.2        
  [6] splines_4.2.1          BiocParallel_1.30.3    GenomeInfoDb_1.32.4    digest_0.6.29          yulab.utils_0.0.5     
 [11] htmltools_0.5.3        GOSemSim_2.22.0        viridis_0.6.2          GO.db_3.15.0           fansi_1.0.3           
 [16] magrittr_2.0.3         memoise_2.0.1          googlesheets4_1.0.1    tzdb_0.3.0             Biostrings_2.64.1     
 [21] graphlayouts_0.8.2     modelr_0.1.9           colorspace_2.0-3       blob_1.2.3             rvest_1.0.3           
 [26] haven_2.5.1            xfun_0.33              crayon_1.5.2           RCurl_1.98-1.9         jsonlite_1.8.2        
 [31] glue_1.6.2             polyclip_1.10-0        gtable_0.3.1           gargle_1.2.1           zlibbioc_1.42.0       
 [36] XVector_0.36.0         scales_1.2.1           DOSE_3.22.1            DBI_1.1.3              Rcpp_1.0.9            
 [41] viridisLite_0.4.1      gridGraphics_0.5-1     bit_4.0.4              htmlwidgets_1.5.4      httr_1.4.4            
 [46] RColorBrewer_1.1-3     ellipsis_0.3.2         pkgconfig_2.0.3        farver_2.1.1           dbplyr_2.2.1          
 [51] utf8_1.2.2             ggplotify_0.1.0        tidyselect_1.2.0       rlang_1.0.6            munsell_0.5.0         
 [56] cellranger_1.1.0       tools_4.2.1            cachem_1.0.6           downloader_0.4         cli_3.4.1             
 [61] generics_0.1.3         RSQLite_2.2.18         broom_1.0.1            evaluate_0.17          fastmap_1.1.0         
 [66] knitr_1.40             bit64_4.0.5            fs_1.5.2               tidygraph_1.2.2        KEGGREST_1.36.3       
 [71] ggraph_2.1.0           aplot_0.1.8            DO.db_2.9              xml2_1.3.3             compiler_4.2.1        
 [76] rstudioapi_0.14        png_0.1-7              reprex_2.0.2           tweenr_2.0.2           stringi_1.7.8         
 [81] lattice_0.20-45        Matrix_1.5-1           vctrs_0.4.2            pillar_1.8.1           lifecycle_1.0.3       
 [86] data.table_1.14.2      bitops_1.0-7           patchwork_1.1.2        qvalue_2.28.0          R6_2.5.1              
 [91] gridExtra_2.3          codetools_0.2-18       MASS_7.3-58.1          assertthat_0.2.1       withr_2.5.0           
 [96] GenomeInfoDbData_1.2.8 parallel_4.2.1         hms_1.1.2              grid_4.2.1             ggfun_0.0.7           
[101] googledrive_2.0.0      ggforce_0.4.1          lubridate_1.8.0

I suggest trying the binaries we've started building on a Mac M1 for Bioconductor devel: https://bioconductor.org/checkResults/3.16/bioc-mac-arm64-LATEST/. We're still working out issues with the M1 builds and we have not yet to my knowledge had anyone try it on an M2, so it will be interesting to know how it works out.

There's two problems here. First you appear unable to query the Bioconductor repository, so you cannot even download the packages you are requesting. That may be a temporal issue, and you should try again. Second, you are saying 'yes' to the installation of a source package on an M2 machine. Don't do that. It took until recently for people who are in the know to compile packages on M2, so trying to do that yourself is just asking for problems.