Question

Error with untar2 that blocks the installation of GO.db on Windows (R 3.5, Bioc 3.8) for using clusterProfiler

0

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Leonardo Collado Torres ★ 1.1k

@lcolladotor

Last seen 13 days ago

United States

Hi,

A colleague of mine (RS) is trying to install the clusterProfiler package that depends on GO.db on his Windows laptop using R 3.5 and Bioconductor 3.8. We haven't been able to install it via BiocManager::install() due to an error with untar2(). If we download the source .tar.gz file on my macOS laptop, uncompress it, copy the contents to the Windows laptop and try installing with R CMD INSTALL GO.db we then get a second type of error.

A second colleague (EB) installed R 3.5 (a fresh install) on her Windows laptop and was able to install clusterProfiler with BiocManager::install().

I have no idea what difference between the 2 Windows computers is affecting the installation and would appreciate any leads on where to look next. My colleague RS has:

Disabled his antivirus
Checked the permissions of his R installation directory
Has WinRAR associated with .gz files.
If he searches for tar.exe he has 2 versions. One under Rtools and another one in elsewhere.

The issue with untar2() also affects RS's ability to install the latest version of rcmdcheck. I'm hoping that if we are able to resolve the untar2() problem, then everything will work. That is, I hope we don't run into the second problem Error: object 'ÿ_' not found.

In this gist https://gist.github.com/lcolladotor/fb4de1d002e0b200302a51c9c10f0e3d you can find all the code and R session information for both RS and EB. Note that both are using BiocManager version 1.30.4. In general RS has no problems installing Windows binary versions of packages, but GO.db is only available via source at https://bioconductor.org/packages/3.8/data/annotation/src/contrib/GO.db_3.7.0.tar.gz.

Let us know if there's any other piece of information we could give you that would be helpful.

Thanks, Leo

go.db clusterprofiler • 1.7k views

ADD COMMENT • link updated 5.9 years ago by Martin Morgan 25k • written 5.9 years ago by Leonardo Collado Torres ★ 1.1k

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RS has a 2nd Windows computer and with a fresh install of R 3.5.1 and Bioconductor 3.8 he got a different error:

R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]

> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> BiocManager::install("clusterProfiler", version = "3.8")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'clusterProfiler'
also installing the dependency ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/clusterProfiler_3.10.0.zip'
Content type 'application/zip' length 981655 bytes (958 KB)
downloaded 958 KB

package ‘clusterProfiler’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\Lieber Institute\AppData\Local\Temp\Rtmp6hQMxy\downloaded_packages
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/GO.db_3.7.0.tar.gz'
Content type 'application/x-gzip' length 31820876 bytes (30.3 MB)
downloaded 30.3 MB

Error in getOctD(x, offset, len) : invalid octal digit
In R CMD INSTALL

The downloaded source packages are in
        ‘C:\Users\Lieber Institute\AppData\Local\Temp\Rtmp6hQMxy\downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘GO.db’ had non-zero exit status
>

I really don't have any clues on what is the cause of all these issues. =/

ADD REPLY • link 5.9 years ago Leonardo Collado Torres ★ 1.1k

score 1 · Answer 1 · 2018-11-30

1

Entering edit mode

Martin Morgan 25k

@martin-morgan-1513

Last seen 3 months ago

United States

Minor speculation but (a) R will not be using a system tar and (b) are spaces in the user name 'Lieber Institute' a problem? Can the latter be overcome with an alias of some kind?

ADD COMMENT • link 5.9 years ago Martin Morgan 25k