Updating Out of Date BiocManager Packages
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Entering edit mode
bs14ab • 0
@bs14ab-23532
Last seen 14 months 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When I run BiocManager::valid(), it tells me 3 packages are out of date, however when I try to update them it doesn't work, I' m not sure why!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               
>
biocmanager valid update packages • 340 views
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0
Entering edit mode

Answer 'no' when asked if you want to install from source.

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I tried both Yes and No and neither worked, what exactly does this mean?

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1
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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'?

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Entering edit mode
@kevin
Last seen 3 hours ago
Republic of Ireland

I think that you need to install Xcode on your Mac. Try this in a terminal and then let us know if it works:

xcode-select --install

Kevin

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Entering edit mode

Hi Kevin, that worked!! Thank you so much :)

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