Entering edit mode
Hello. I can't load ensembldb and EnsDb.Hsapiens.v86. Please see the requested information below. Thank you in advance for any and all advice.
BiocManager::install("ensembldb")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://ftp.osuosl.org/pub/cran
BioCsoft: https://bioconductor.org/packages/3.15/bioc
BioCann: https://bioconductor.org/packages/3.15/data/annotation
BioCexp: https://bioconductor.org/packages/3.15/data/experiment
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Old packages: 'colorspace', 'Matrix'
Update all/some/none? [a/s/n]:
a
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2:
cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://R-Forge.R-project.org/bin/macosx/contrib/4.2:
cannot open URL 'https://R-Forge.R-project.org/bin/macosx/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://www.rforge.net/bin/macosx/contrib/4.2:
cannot open URL 'https://www.rforge.net/bin/macosx/contrib/4.2/PACKAGES'
There are binary versions available but the source versions are later:
binary source needs_compilation
colorspace 2.0-3 2.1-0 TRUE
Matrix 1.4-1 1.4-2 TRUE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) y
installing the source packages ‘colorspace’, ‘Matrix’
trying URL 'https://R-Forge.R-project.org/src/contrib/colorspace_2.1-0.tar.gz'
Content type 'application/x-gzip' length 2464234 bytes (2.4 MB)
==================================================
downloaded 2.4 MB
trying URL 'https://R-Forge.R-project.org/src/contrib/Matrix_1.4-2.tar.gz'
Content type 'application/x-gzip' length 3673197 bytes (3.5 MB)
==================================================
downloaded 3.5 MB
* installing *source* package ‘colorspace’ ...
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘colorspace’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/colorspace’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/colorspace’
* installing *source* package ‘Matrix’ ...
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘Matrix’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Matrix’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Matrix’
The downloaded source packages are in
‘/private/var/folders/fn/9ftb5p2156389n_frl68stz40000gn/T/Rtmpxf3yAQ/downloaded_packages’
Warning messages:
1: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'ensembldb'
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘colorspace’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘Matrix’ had non-zero exit status
>
BiocManager::install("EnsDb.Hsapiens.v86")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://ftp.osuosl.org/pub/cran
BioCsoft: https://bioconductor.org/packages/3.15/bioc
BioCann: https://bioconductor.org/packages/3.15/data/annotation
BioCexp: https://bioconductor.org/packages/3.15/data/experiment
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Installing package(s) 'EnsDb.Hsapiens.v86'
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2:
cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://R-Forge.R-project.org/bin/macosx/contrib/4.2:
cannot open URL 'https://R-Forge.R-project.org/bin/macosx/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://www.rforge.net/bin/macosx/contrib/4.2:
cannot open URL 'https://www.rforge.net/bin/macosx/contrib/4.2/PACKAGES'
installing the source package ‘EnsDb.Hsapiens.v86’
trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/EnsDb.Hsapiens.v86_2.99.0.tar.gz'
Content type 'application/x-gzip' length 78178992 bytes (74.6 MB)
==================================================
downloaded 74.6 MB
* installing *source* package ‘EnsDb.Hsapiens.v86’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘AnnotationDbi’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘png’
Execution halted
ERROR: lazy loading failed for package ‘EnsDb.Hsapiens.v86’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/EnsDb.Hsapiens.v86’
The downloaded source packages are in
‘/private/var/folders/fn/9ftb5p2156389n_frl68stz40000gn/T/Rtmpxf3yAQ/downloaded_packages’
Old packages: 'colorspace', 'Matrix'
Update all/some/none? [a/s/n]:
a
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2:
cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://R-Forge.R-project.org/bin/macosx/contrib/4.2:
cannot open URL 'https://R-Forge.R-project.org/bin/macosx/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://www.rforge.net/bin/macosx/contrib/4.2:
cannot open URL 'https://www.rforge.net/bin/macosx/contrib/4.2/PACKAGES'
There are binary versions available but the source versions are later:
binary source needs_compilation
colorspace 2.0-3 2.1-0 TRUE
Matrix 1.4-1 1.4-2 TRUE
Warning message:
In install.packages(...) :
installation of package ‘EnsDb.Hsapiens.v86’ had non-zero exit status
RESULTS of sessionInfo( )
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.4
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] BiocManager_1.30.18 Biobase_2.56.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 IRanges_2.30.0
[6] S4Vectors_0.34.0 BiocGenerics_0.42.0 tximport_1.24.0 forcats_0.5.1 stringr_1.4.0
[11] dplyr_1.0.9 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.7
[16] ggplot2_3.3.6 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] httr_1.4.3 bit64_4.0.5 jsonlite_1.8.0 modelr_0.1.8
[5] assertthat_0.2.1 blob_1.2.3 GenomeInfoDbData_1.2.8 cellranger_1.1.0
[9] pillar_1.7.0 RSQLite_2.2.14 backports_1.4.1 glue_1.6.2
[13] XVector_0.36.0 rvest_1.0.2 colorspace_2.0-3 pkgconfig_2.0.3
[17] broom_1.0.0 haven_2.5.0 zlibbioc_1.42.0 scales_1.2.0
[21] tzdb_0.3.0 generics_0.1.2 ellipsis_0.3.2 cachem_1.0.6
[25] withr_2.5.0 cli_3.3.0 magrittr_2.0.3 crayon_1.5.1
[29] readxl_1.4.0 memoise_2.0.1 fs_1.5.2 fansi_1.0.3
[33] xml2_1.3.3 tools_4.2.1 hms_1.1.1 lifecycle_1.0.1
[37] munsell_0.5.0 reprex_2.0.1 compiler_4.2.1 rlang_1.0.3
[41] grid_4.2.1 RCurl_1.98-1.7 rstudioapi_0.13 bitops_1.0-7
[45] gtable_0.3.0 DBI_1.1.3 R6_2.5.1 lubridate_1.8.0
[49] fastmap_1.1.0 bit_4.0.4 utf8_1.2.2 stringi_1.7.6
[53] Rcpp_1.0.8.3 vctrs_0.4.1 dbplyr_2.2.1 tidyselect_1.1.2
I agree with mbk0asis above - you should first install the
pngpackage and maybe also avoid installing packages from source as your system seems to lack required compilers:And select to install binary packages instead of installing them from source.