Problems installing DESeq2
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@2245a5cf
Last seen 24 days ago
Sweden

Hello,

I suddenly got problem installing DESeq2 and would really appreciate help. The issue seems to be packages cache, data.table and xfun that can't be updated to their newest version.

I use RStudio 1.4.1106.

I start the installation with this:

BiocManager::install("DESeq2") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com/

Bioconductor version 3.10 (BiocManager 1.30.15), R 3.6.3 (2020-02-29) Old packages: 'cachem', 'data.table', 'xfun' Update all/some/none? [a/s/n]: a

There are binary versions available but the source versions are later: binary source needs_compilation cachem 1.0.4 1.0.5 TRUE data.table 1.13.6 1.14.0 TRUE xfun 0.22 0.23 TRUE

Do you want to install from sources the packages which need compilation? (Yes/no/cancel) yes installing the source packages ‘cachem’, ‘data.table’, ‘xfun’

For the three packages I get following error:

installing source package ‘cachem’ ... package ‘cachem’ 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 ‘cachem’

  • removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cachem’
  • restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cachem’

And later on also this error:

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

Warning messages: 1: package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'DESeq2' 2: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘cachem’ had non-zero exit status

Does anyone have a clue on what is wrong? Thank you in advance!

Isabelle

DESeq2 • 274 views
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I assume you are on macOS? Did you install XCode, as the xcrun error indicates you have not.

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Thank you for the help!

It makes sense. I have an old Mac and no XCode installed. It is strange though because installing DESeq was not a problem a few days ago.

I tried now to install XCode but it seems to be problematic with my old computer. Time to get a new computer I think…

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@kevin
Last seen 10 minutes ago
Naas, Republic of Ireland

Hi, please try the solution suggested here: Avoid upgrading BiocManager to 1.30.13; fix proposed

Kevin

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Thank you for your reply! I will try their suggestions!

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