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
gfortran seems to not be installed, you may follow this tutorial : https://www.cynkra.com/blog/2021-03-16-gfortran-macos/