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bs14ab
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@bs14ab-23532
Last seen 3.8 years ago
When I run BiocManager::valid(), it tells me 3 packages are out of date, however when I try to update them it doesn't work, I' m not sure why! Please see the code below. I am only just learning how to use Bioconductor, so I apologise if this is something obvious!
BiocManager::valid()
* sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] AnnotationHub_2.20.0 BiocFileCache_1.12.0 dbplyr_1.4.3 GenomicRanges_1.40.0 GenomeInfoDb_1.24.0 IRanges_2.22.1
[7] S4Vectors_0.26.0 BiocGenerics_0.34.0 oligoClasses_1.50.0
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.18.1 tidyselect_1.1.0 BiocVersion_3.11.1 purrr_0.3.4
[5] lattice_0.20-41 vctrs_0.2.4 htmltools_0.4.0 yaml_2.2.1
[9] interactiveDisplayBase_1.26.0 blob_1.2.1 rlang_0.4.6 later_1.0.0
[13] pillar_1.4.4 glue_1.4.0 DBI_1.1.0 rappdirs_0.3.1
[17] bit64_0.9-7 affyio_1.58.0 matrixStats_0.56.0 GenomeInfoDbData_1.2.3
[21] foreach_1.5.0 lifecycle_0.2.0 zlibbioc_1.34.0 Biostrings_2.56.0
[25] codetools_0.2-16 memoise_1.1.0 Biobase_2.48.0 ff_2.2-14.2
[29] fastmap_1.0.1 httpuv_1.5.2 curl_4.3 AnnotationDbi_1.50.0
[33] Rcpp_1.0.4.6 xtable_1.8-4 promises_1.1.0 BiocManager_1.30.10
[37] DelayedArray_0.14.0 XVector_0.28.0 mime_0.9 bit_1.1-15.2
[41] digest_0.6.25 dplyr_0.8.5 shiny_1.4.0.2 grid_4.0.0
[45] tools_4.0.0 bitops_1.0-6 magrittr_1.5 RCurl_1.98-1.2
[49] tibble_3.0.1 RSQLite_2.2.0 crayon_1.3.4 pkgconfig_2.0.3
[53] ellipsis_0.3.0 Matrix_1.2-18 assertthat_0.2.1 httr_1.4.1
[57] rstudioapi_0.11 iterators_1.0.12 R6_2.4.1 compiler_4.0.0
.
Bioconductor version '3.11'
* 3 packages out-of-date
* 0 packages too new
create a valid installation with
BiocManager::install(c(
"backports", "glue", "vctrs"
), update = TRUE, ask = FALSE)
more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
Warning message:
3 packages out-of-date; 0 packages too new
> BiocManager::install(c(
+ "backports", "glue", "vctrs"
+ ), update = TRUE, ask = FALSE)
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'backports', 'glue', 'vctrs'
There are binary versions available but the source versions are later:
binary source needs_compilation
backports 1.1.6 1.1.7 TRUE
glue 1.4.0 1.4.1 TRUE
vctrs 0.2.4 0.3.0 TRUE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) yes
installing the source packages ‘backports’, ‘glue’, ‘vctrs’
trying URL 'https://cran.rstudio.com/src/contrib/backports_1.1.7.tar.gz'
Content type 'application/x-gzip' length 17676 bytes (17 KB)
==================================================
downloaded 17 KB
trying URL 'https://cran.rstudio.com/src/contrib/glue_1.4.1.tar.gz'
Content type 'application/x-gzip' length 98581 bytes (96 KB)
==================================================
downloaded 96 KB
trying URL 'https://cran.rstudio.com/src/contrib/vctrs_0.3.0.tar.gz'
Content type 'application/x-gzip' length 883312 bytes (862 KB)
==================================================
downloaded 862 KB
* installing *source* package ‘backports’ ...
** package ‘backports’ successfully unpacked and MD5 sums checked
** 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 ‘backports’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/backports’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/backports’
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** 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 ‘glue’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/glue’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/glue’
* installing *source* package ‘vctrs’ ...
** package ‘vctrs’ successfully unpacked and MD5 sums checked
** 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 ‘vctrs’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/vctrs’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/vctrs’
The downloaded source packages are in
‘/private/var/folders/9s/4mdrj_ld2b39y0t_7v5zrs_w0000gn/T/RtmpST3OES/downloaded_packages’
Old packages: 'backports', 'glue', 'vctrs'
There are binary versions available but the source versions are later:
binary source needs_compilation
backports 1.1.6 1.1.7 TRUE
glue 1.4.0 1.4.1 TRUE
vctrs 0.2.4 0.3.0 TRUE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) yes
installing the source packages ‘backports’, ‘glue’, ‘vctrs’
trying URL 'https://cran.rstudio.com/src/contrib/backports_1.1.7.tar.gz'
Content type 'application/x-gzip' length 17676 bytes (17 KB)
==================================================
downloaded 17 KB
trying URL 'https://cran.rstudio.com/src/contrib/glue_1.4.1.tar.gz'
Content type 'application/x-gzip' length 98581 bytes (96 KB)
==================================================
downloaded 96 KB
trying URL 'https://cran.rstudio.com/src/contrib/vctrs_0.3.0.tar.gz'
Content type 'application/x-gzip' length 883312 bytes (862 KB)
==================================================
downloaded 862 KB
* installing *source* package ‘backports’ ...
** package ‘backports’ successfully unpacked and MD5 sums checked
** 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 ‘backports’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/backports’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/backports’
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** 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 ‘glue’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/glue’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/glue’
* installing *source* package ‘vctrs’ ...
** package ‘vctrs’ successfully unpacked and MD5 sums checked
** 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 ‘vctrs’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/vctrs’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/vctrs’
The downloaded source packages are in
‘/private/var/folders/9s/4mdrj_ld2b39y0t_7v5zrs_w0000gn/T/RtmpST3OES/downloaded_packages’
Warning messages:
1: In install.packages(...) :
installation of package ‘backports’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘glue’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘vctrs’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘backports’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘glue’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘vctrs’ had non-zero exit status
Here is my session info:
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] AnnotationHub_2.20.0 BiocFileCache_1.12.0 dbplyr_1.4.3 GenomicRanges_1.40.0 GenomeInfoDb_1.24.0 IRanges_2.22.1
[7] S4Vectors_0.26.0 BiocGenerics_0.34.0 oligoClasses_1.50.0
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.18.1 tidyselect_1.1.0 BiocVersion_3.11.1 purrr_0.3.4
[5] lattice_0.20-41 vctrs_0.2.4 htmltools_0.4.0 yaml_2.2.1
[9] interactiveDisplayBase_1.26.0 blob_1.2.1 rlang_0.4.6 later_1.0.0
[13] pillar_1.4.4 glue_1.4.0 DBI_1.1.0 rappdirs_0.3.1
[17] bit64_0.9-7 affyio_1.58.0 matrixStats_0.56.0 GenomeInfoDbData_1.2.3
[21] foreach_1.5.0 lifecycle_0.2.0 zlibbioc_1.34.0 Biostrings_2.56.0
[25] codetools_0.2-16 memoise_1.1.0 Biobase_2.48.0 ff_2.2-14.2
[29] fastmap_1.0.1 httpuv_1.5.2 curl_4.3 AnnotationDbi_1.50.0
[33] Rcpp_1.0.4.6 xtable_1.8-4 promises_1.1.0 BiocManager_1.30.10
[37] DelayedArray_0.14.0 XVector_0.28.0 mime_0.9 bit_1.1-15.2
[41] digest_0.6.25 dplyr_0.8.5 shiny_1.4.0.2 grid_4.0.0
[45] tools_4.0.0 bitops_1.0-6 magrittr_1.5 RCurl_1.98-1.2
[49] tibble_3.0.1 RSQLite_2.2.0 crayon_1.3.4 pkgconfig_2.0.3
[53] ellipsis_0.3.0 Matrix_1.2-18 assertthat_0.2.1 httr_1.4.1
[57] rstudioapi_0.11 iterators_1.0.12 R6_2.4.1 compiler_4.0.0
>
Answer 'no' when asked if you want to install from source.
I tried both Yes and No and neither worked, what exactly does this mean?
probably answering 'no' lead to a failure in different ways. Generally installing from 'source' requires additional software, which you installed following Kevin's advice. But the additional software required may be quite a bit more complicated, and users will often not have permissions to install the necessary software on their (e.g., university-managed) computer. So it is usually better to answer 'no'.
How did the installation fail when you answered 'no'?