installation of package ‘GenomeInfoDbData’ had non-zero exit status
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N.D.Hubot • 0
@user-24140
Last seen 3.4 years ago

Hello,

I am struggling a lot to install the "GenomeInfoDbData" package. I don't know what is wrong but I think it might be related to the dependency with the package "colorspace". Do you have an idea about how I could install it?

Thanks in advance for your answer.

Code should be placed in three backticks as shown below

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("GenomeInfoDbData")

> BiocManager::install("GenomeInfoDbData")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'GenomeInfoDbData'
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/GenomeInfoDbData_1.2.4.tar.gz'
Content type 'application/x-gzip' length 10673545 bytes (10.2 MB)
downloaded 10.2 MB


The downloaded source packages are in
    ‘C:\Users\ndh1n17\AppData\Local\Temp\RtmpMXYzOd\downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status
GenomeInfoDbData "GenomeInfoDbData"package • 4.4k views
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Entering edit mode

Was this the complete output? Was there a warning or ERROR that lead you to believe that it was colorspace? You could try just installing colorspace to see if there is an ERROR. BiocManager::install will install any CRAN or Bioconductor so you could try BiocManager::install('colorspace') and if installs correctly then try GenomeInfoDbData again. If you continue to have trouble, could you also try BiocManager::valid() to see what the output of that says as well as any additional output from the install call.

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Hi shepherl, Thanks for your answer. Yes that was the complete output. I was suspecting colorspace was responsible because I was struggling to install it too and had dependencies problems affecting the loading of ggplot2 and dada2. Now I have managed to install the old version of colorspace but I am still able to install the GenomeInfoDbData package.

Below is the output. I have tried to run the command suggested in the BiocManager::valid() but it is still not installing.

    BiocManager::valid()

* sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.3      tools_4.0.3         knitr_1.30          xfun_0.19          

Bioconductor version '3.12'

  * 3 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install(c(
    "colorspace", "lubridate", "xlsx"
  ), 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(
+     "colorspace", "lubridate", "xlsx"
+ ), update = TRUE, ask = FALSE)
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'colorspace', 'lubridate', 'xlsx'

  There are binary versions available but the source versions are later:
            binary  source needs_compilation
colorspace   1.4-1   2.0-0              TRUE
lubridate    1.7.9 1.7.9.2              TRUE
xlsx       0.6.4.2   0.6.5             FALSE

installing the source packages ‘colorspace’, ‘lubridate’, ‘xlsx’

trying URL 'https://cran.rstudio.com/src/contrib/colorspace_2.0-0.tar.gz'
Content type 'application/x-gzip' length 2203295 bytes (2.1 MB)
downloaded 2.1 MB

trying URL 'https://cran.rstudio.com/src/contrib/lubridate_1.7.9.2.tar.gz'
Content type 'application/x-gzip' length 472640 bytes (461 KB)
downloaded 461 KB

trying URL 'https://cran.rstudio.com/src/contrib/xlsx_0.6.5.tar.gz'
Content type 'application/x-gzip' length 489493 bytes (478 KB)
downloaded 478 KB


The downloaded source packages are in
    ‘C:\Users\ndh1n17\AppData\Local\Temp\RtmpS82PdG\downloaded_packages’
Installation path not writeable, unable to update packages: codetools, KernSmooth, nlme
Old packages: 'colorspace', 'lubridate', 'xlsx'

  There are binary versions available but the source versions are later:
            binary  source needs_compilation
colorspace   1.4-1   2.0-0              TRUE
lubridate    1.7.9 1.7.9.2              TRUE
xlsx       0.6.4.2   0.6.5             FALSE

installing the source packages ‘colorspace’, ‘lubridate’, ‘xlsx’

trying URL 'https://cran.rstudio.com/src/contrib/colorspace_2.0-0.tar.gz'
Content type 'application/x-gzip' length 2203295 bytes (2.1 MB)
downloaded 2.1 MB

trying URL 'https://cran.rstudio.com/src/contrib/lubridate_1.7.9.2.tar.gz'
Content type 'application/x-gzip' length 472640 bytes (461 KB)
downloaded 461 KB

trying URL 'https://cran.rstudio.com/src/contrib/xlsx_0.6.5.tar.gz'
Content type 'application/x-gzip' length 489493 bytes (478 KB)
downloaded 478 KB


The downloaded source packages are in
    ‘C:\Users\ndh1n17\AppData\Local\Temp\RtmpS82PdG\downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘colorspace’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘lubridate’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘xlsx’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘colorspace’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘lubridate’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘xlsx’ had non-zero exit status
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Do you have Rtools installed? Without that you won't be able to install source packages on Windows.

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yes I have Rtools 4.0 installed

Sys.which("make")
                          make

"C:\rtools40\usr\bin\make.exe"

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Did you ever find a solution to this? I am having a similar issue and I have Rtools 4.0 installed.

ADD REPLY •
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Entering edit mode

Just to clarify: You don't necessarily need Rtools to install source packages on Windows, only if the packages to install need compilation. However, _data_ packages (annotation or experiment) never need compilation so Rtools is not required for any of them (this includes GenomeInfoDbData). This is why we don't produce Windows or Mac binaries for these packages.

H.

ADD REPLY •
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Entering edit mode

Can you post the full output of what you are seeing?

Also, if you have old installations of packages in other directories that you don't have write access to, R will try to update them.

This may have been fixed / hidden in newer versions of BiocManager.

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