[Bioc-devel] Fwd: TDbasedUFE problems reported in the Multiple platform build/check report for BioC 3.17

Tue Mar 7 15:23:30 CET 2023

Hi Tag,

Yes, I have been trying to resolve issues with Pandoc on our build machines. I know this affected your build report and others. Since you're going through a package review, you'll likely see this resolved sooner on the single package report. For anyone who is looking at the build reports, it will be resolved on Wednesday's report.

Jennifer Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Y-h. Taguchi <tag using granular.com>
Sent: Tuesday, March 7, 2023 8:10 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Fwd: TDbasedUFE problems reported in the Multiple platform build/check report for BioC 3.17

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Dear People,

Although I have received the following error message, it might not be
because of my side
The reasons why I thinks so are

1) The error  is

>Could not find executable pandoc-citeproc

This means that the system that tries to build is missing pandoc.

2) many other packages receive the same error. Here are some examples

Multiple platform build/check report for BioC 3.17 - BUILD results for BG2
on nebbiolo1 (bioconductor.org)
<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_BG2_nebbiolo1-2Dbuildsrc.html&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=I5Sw5JzBx8K6loFZY3AYVvZX8IfWJ4Au7Hsa65WUiOgfwprbceTNkissdG8hk5f2&s=rTl4QTHfTCVAk4tF1Hqn3gF7kVaEd1aqokt_PDyL26Y&e= >
Multiple platform build/check report for BioC 3.17 - BUILD results for
planttfhunter on nebbiolo1 (bioconductor.org)
<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_planttfhunter_nebbiolo1-2Dbuildsrc.html&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=I5Sw5JzBx8K6loFZY3AYVvZX8IfWJ4Au7Hsa65WUiOgfwprbceTNkissdG8hk5f2&s=hgAyDMpoNzjzUXOAGfYsLp0AW2f-ip7-8wMfCq36IgU&e= >
Multiple platform build/check report for BioC 3.17 - BUILD results for
MetaPhOR on nebbiolo1 (bioconductor.org)
<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_MetaPhOR_nebbiolo1-2Dbuildsrc.html&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=I5Sw5JzBx8K6loFZY3AYVvZX8IfWJ4Au7Hsa65WUiOgfwprbceTNkissdG8hk5f2&s=dEtwOE6mblSAZVbAJzRpgZjL0APrTbDjlU9GS16eCk8&e= >

3) I did not commit anything since it has passed the build test last time.

Is it possible for you to check if your system that performs build is OK or
not?

Yours, tag.

---------- Forwarded message ---------
From: <BBS-noreply using bioconductor.org>
Date: 2023$BG/(B3$B7n(B7$BF|(B($B2P(B) 2:06
Subject: TDbasedUFE problems reported in the Multiple platform build/check
report for BioC 3.17
To: <tag using granular.com>

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

Hi TDbasedUFE maintainer,

According to the Multiple platform build/check report for BioC 3.17,
the TDbasedUFE package has the following problem(s):

  o ERROR for 'R CMD build' on nebbiolo1. See the details here:

https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.17_bioc-2DLATEST_TDbasedUFE_nebbiolo1-2Dbuildsrc.html&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=I5Sw5JzBx8K6loFZY3AYVvZX8IfWJ4Au7Hsa65WUiOgfwprbceTNkissdG8hk5f2&s=NgRAs3gpRQ7oz-bAocvNL3Ic7-gy2-r1QUX8ewU_Gec&e=

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
    you do so several days after you received this email.

  * It is possible that the problems reported in this report are false
positives,
    either because another package (from CRAN or Bioconductor) breaks your
    package (if yours depends on it) or because of a Build System problem.
    If this is the case, then you can ignore this email.

  * Please check the report again 24h after you've committed your changes
to the
    package and make sure that all the problems have gone.

  * If you have questions about this report or need help with the
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Thanks for contributing to the Bioconductor project!

--
Y-h. Taguchi, Dept. Phys., Chuo Univ., Kasuga, Bunkyo-ku, Tokyo
112-8551,Japan
Tel./Fax.  +81-3-3817-1791/1792 https://urldefense.proofpoint.com/v2/url?u=https-3A__researchmap.jp_Yh-5FTaguchi_&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=I5Sw5JzBx8K6loFZY3AYVvZX8IfWJ4Au7Hsa65WUiOgfwprbceTNkissdG8hk5f2&s=0FUS-g5Xuq0DSkz5FeAXUrgs-2DFZiFucvb0mbYdxKk&e=
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