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[Bioc-devel] Fwd: TissueEnrich problems reported in the Multiple platform build/check report for BioC 3.9

4 messages · Ashish Jain, Shepherd, Lori, Hervé Pagès

#
Hi All,

I just got the message that my package is giving an error during the build
process on Bioconductor build server. I saw the logs and found it is
failing while building the vignette. I am not sure why it's happening as I
have not updated the package since release and it was building without any
errors. Can someone look into this?

Regards,
Ashish Jain

---------- Forwarded message ---------
From: <BBS-noreply at bioconductor.org>
Date: Mon, Sep 16, 2019 at 1:59 PM
Subject: TissueEnrich problems reported in the Multiple platform
build/check report for BioC 3.9
To: <jain at iastate.edu>


[This is an automatically generated email. Please don't reply.]

Hi TissueEnrich maintainer,

According to the Multiple platform build/check report for BioC 3.9,
the TissueEnrich package has the following problem(s):

  o ERROR for 'R CMD build' on malbec2. See the details here:

https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/TissueEnrich/malbec2-buildsrc.html

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org

Notes:

  * This was the status of your package at the time this email was sent to
you.
    Given that the online report is updated daily (in normal conditions) you
    could see something different when you visit the URL(s) above,
especially if
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  * It is possible that the problems reported in this report are false
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    either because another package (from CRAN or Bioconductor) breaks your
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  * Please check the report again 24h after you've committed your changes
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#
I am able to reproduce the ERROR.  It seems to be an issue of trying to subset.
Tissue             value
1 Adipose Tissue  1.63226821549951
2 Adipose Tissue                 0
3 Adipose Tissue                 0
4 Adipose Tissue 0.485426827170242
5 Adipose Tissue 0.584962500721156
6 Adipose Tissue  3.05311133645956
Error: 1 components of `...` had unexpected names.

We detected these problematic arguments:
* `Tissue`

Did you misspecify an argument?
Call `rlang::last_error()` to see a backtrace
You can see if there were any recent changes to package you depend on that could have caused this.  A package you depend on may have changed their functionality.  I needed to update packages (with BiocManager::install()   update all )  in order to reproduce.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
#
Hi Lori,

Thank you for your help. I was able to reproduce the issue locally after
updating the packages. I updated the vignette with the changes and pushed
it on both RELEASE_3_9 and the development (3_10) branches. Again thank you
for your help!

Regards,
Ashish Jain

On Tue, Sep 17, 2019 at 7:06 AM Shepherd, Lori <
Lori.Shepherd at roswellpark.org> wrote:

            

  
    
#
Thanks Ashish for the quick fix.

For the record the change to tidyr::gather() in the latest version of 
tidyr (v 1.0.0) also breaks the CNPBayes and SummarizedBenchmark packages:

 
https://bioconductor.org/checkResults/3.9/bioc-LATEST/CNPBayes/malbec2-buildsrc.html

 
https://bioconductor.org/checkResults/3.9/bioc-LATEST/SummarizedBenchmark/malbec2-buildsrc.html

Also FWIW the man page for gather() actually recommends to switch to 
pivot_longer():

   Description:

      *Retired*

      Development on ?gather()? is complete, and for new code we
      recommend switching to ?pivot_longer()?, which is easier to use,
      more featureful, and still under active development. ?df %>%
      gather("key", "value", x, y, z)? is equivalent to ?df %>%
      pivot_longer(c(x, y, z), names_to = "key", values_to = "value")?

      See more details in ?vignette("pivot")?.

Cheers,
H.
On 9/17/19 09:17, Ashish Jain wrote: