non-zero exit status when installing dependency packages

[RemyMG]

Hello Adriano,

I'm not sure it's the place for these issues as they are relative to Bioconductor packages but as I'm trying to install the latest version of timaR (2.7.4) I get two error messages when installing GenomeInfoDbData package and updating DelayedArray package.

R version: 4.2.3 Rtools version: rtools42-5355-5357 (I tryed with R version 4.2.2 and older rtools42 version and it doesn't work either).

The error message:

> remotes::install_github("taxonomicallyinformedannotation/tima-r")
Downloading GitHub repo taxonomicallyinformedannotation/tima-r@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                                   
2: CRAN packages only                    
3: None                                  
4: blob         (1.2.3  -> 1.2.4 ) [CRAN]
5: DelayedArray (0.23.2 -> 0.24.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1
GenomeInf... (NA     -> 1.2.9 ) [CRAN]
blob         (1.2.3  -> 1.2.4 ) [CRAN]
DelayedArray (0.23.2 -> 0.24.0) [CRAN]
Installing 3 packages: GenomeInfoDbData, blob, DelayedArray

  There are binary versions available but the source versions are later:
             binary source needs_compilation
blob          1.2.3  1.2.4             FALSE
DelayedArray 0.23.2 0.24.0              TRUE

installing the source packages ‘GenomeInfoDbData’, ‘blob’, ‘DelayedArray’

trying URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz'
Content type 'application/x-gzip' length 11725198 bytes (11.2 MB)
downloaded 11.2 MB

trying URL 'https://cran.rstudio.com/src/contrib/blob_1.2.4.tar.gz'
Content type 'application/x-gzip' length 10620 bytes (10 KB)
downloaded 10 KB

trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/DelayedArray_0.24.0.tar.gz'
Content type 'application/x-gzip' length 642972 bytes (627 KB)
downloaded 627 KB

The downloaded source packages are in
    ‘C:\Users\marcellr\AppData\Local\Temp\RtmpIzI8Yn\downloaded_packages’
Running `R CMD build`...

STDOUT:

STDERR:

Error: Failed to install 'timaR' from GitHub:
  Failed to `R CMD build` package, try `build = FALSE`.
In addition: Warning messages:
1: In i.p(...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status
2: In i.p(...) : installation of package ‘blob’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘DelayedArray’ had non-zero exit status

I also tried with build = FALSE option but its doesn't work better:

> remotes::install_github("taxonomicallyinformedannotation/tima-r", build = FALSE)
Downloading GitHub repo taxonomicallyinformedannotation/tima-r@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                                   
2: CRAN packages only                    
3: None                                  
4: blob         (1.2.3  -> 1.2.4 ) [CRAN]
5: DelayedArray (0.23.2 -> 0.24.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1
GenomeInf... (NA     -> 1.2.9 ) [CRAN]
blob         (1.2.3  -> 1.2.4 ) [CRAN]
DelayedArray (0.23.2 -> 0.24.0) [CRAN]
Installing 3 packages: GenomeInfoDbData, blob, DelayedArray

  There are binary versions available but the source versions are later:
             binary source needs_compilation
blob          1.2.3  1.2.4             FALSE
DelayedArray 0.23.2 0.24.0              TRUE

installing the source packages ‘GenomeInfoDbData’, ‘blob’, ‘DelayedArray’

trying URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz'
Content type 'application/x-gzip' length 11725198 bytes (11.2 MB)
downloaded 11.2 MB

trying URL 'https://cran.rstudio.com/src/contrib/blob_1.2.4.tar.gz'
Content type 'application/x-gzip' length 10620 bytes (10 KB)
downloaded 10 KB

trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/DelayedArray_0.24.0.tar.gz'
Content type 'application/x-gzip' length 642972 bytes (627 KB)
downloaded 627 KB

The downloaded source packages are in
    ‘C:\Users\marcellr\AppData\Local\Temp\RtmpIzI8Yn\downloaded_packages’
Warning messages:
1: In i.p(...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status
2: In i.p(...) : installation of package ‘blob’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘DelayedArray’ had non-zero exit status
4: In i.p(...) :
  installation of package ‘C:/Users/marcellr/AppData/Local/Temp/RtmpIzI8Yn/remotes8181a8e690f/taxonomicallyinformedannotation-tima-r-f737ce6’ had non-zero exit status

Does it come from rtools that cannot compile the packages ? Even if I try not to update packages it generates the same error message.

Any help ?

Thanks a lot !

[Adafede]

Hi @RemyMG, by default, I ask for the latest versions of all dependencies, but if this message breaks the build you can simply skip the updates (as suggested either by entering 3 or an empty line to skip)... No idea what is wrong with the sub-dependencies. I am trying to keep the dependencies as slick as possible to avoid this type of issues but well...you know what it is 😊

Tell me if the problem persists, just to see if I have to freeze part of the dependencies to smaller versions until it gets fixed.

And do not hesitate to open issues, any feedback is welcome!

[Adafede]

@RemyMG

As it looks your issue is related to blob, they just released a fix 7hours ago: https://github.com/tidyverse/blob/blob/main/NEWS.md

Might it be related? Can you try installing it first and then the rest?

[Adafede]

@RemyMG Could you test with the latest version? Can I close?

[RemyMG]

Hi, yes you can close. It was actualy a Rtools issue. Now it works fine :)