[Bioc-devel] Fwd: TissueEnrich problems reported in the Multiple platform build/check report for BioC 3.9
Pages, Herve
hp@ge@ @end|ng |rom |redhutch@org
Tue Sep 17 19:25:27 CEST 2019
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:
> 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 using roswellpark.org> wrote:
>
>> I am able to reproduce the ERROR. It seems to be an issue of trying to
>> subset.
>>
>>> head(exp %>% gather(Tissue)) 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> head(exp %>% gather(Tissue=1:(ncol(exp)-1)))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
>> ------------------------------
>> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Ashish
>> Jain <jain using iastate.edu>
>> *Sent:* Monday, September 16, 2019 3:08 PM
>> *To:* bioc-devel using r-project.org <bioc-devel using r-project.org>
>> *Subject:* [Bioc-devel] Fwd: TissueEnrich problems reported in the
>> Multiple platform build/check report for BioC 3.9
>>
>> 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 using 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 using 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://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.9_bioc-2DLATEST_TissueEnrich_malbec2-2Dbuildsrc.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o1sr-o_MvUhGrSGKx6vufW6iDzp84bUofNfcGxAtObw&s=sA7mdXKmscGnnwrA2a-Dh9P7BpaJOuqIdbh1X6qTaAw&e=
>>
>> Please take the time to address this by committing and pushing
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>>
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>> Thanks for contributing to the Bioconductor project!
>>
>>
>>
>> --
>> Regards,
>> Ashish Jain
>> Ph.D. Candidate
>> Bioinformatics and Computational Biology
>> Iowa State University
>> Ph +1-317-529-7973
>> Website: *https://urldefense.proofpoint.com/v2/url?u=https-3A__ashishjain1988.github.io&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o1sr-o_MvUhGrSGKx6vufW6iDzp84bUofNfcGxAtObw&s=EwM1zfwfJ7aRuNkay1qqCrf6BW291hXiN-1fbtIqWYY&e=
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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