[Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

Mon Nov 23 21:29:53 CET 2020

Hi Kern,
I built epihet in my linux system, did not see anything wrong.
 Could you help me?thanks

First, download epihet, and build

(base) [chenx using helix ~]$ git clone https://github.com/TheJacksonLaboratory/epihet.git
Initialized empty Git repository in /home/c-chenx/epihet/.git/
remote: Enumerating objects: 839, done.
remote: Total 839 (delta 0), reused 0 (delta 0), pack-reused 839
Receiving objects: 100% (839/839), 4.59 MiB, done.
Resolving deltas: 100% (449/449), done.
(base) [chenx using helix ~]$ R CMD build epihet
* checking for file ‘epihet/DESCRIPTION’ ... OK
* preparing ‘epihet’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘epihet_1.5.5.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'

Please check the time, I indeed built it again today

(base) [chenx using helix ~]$ ll -a
-rw-r--r--   1 chenx jaxuser     798104 Nov 23 13:34 epihet_1.5.5.tar.gz

AND CHECK IT, ONLY WARINGS , just COMPLAIN THE Compile version,please see attached file for complete check result

R CMD check epihet_1.5.5.tar.gz
WARNINGs: program compiled against libxml 209 using older 207

From: "Kern, Lori" <Lori.Shepherd using RoswellPark.org>
Date: Monday, November 23, 2020 at 12:42 PM
To: Xiaowen Chen <Xiaowen.Chen using jax.org>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

Your packages is failing in both release and devel of Bioconductor.  You need to fix the package.  You can see the ERROR on the build reports

bioconductor.org/checkResults/devel/bioc-LATEST/epihet

and

bioconductor.org/checkResults/release/bioc-LATEST/epihet
If you click on the ERROR on either one of those pages for any of the operating systems it will give more information on how the package is failing.

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Xiaowen Chen <Xiaowen.Chen using jax.org>
Sent: Monday, November 23, 2020 12:19 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] FW: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

Hi Bioconductor,
Recently I received the next email, but I used the website you sent me, version 1.7 looks fine after three days when I submitted :
 bioconductor.org/checkResults/devel/bioc-LATEST/epihet/.
 And I can find my package on the following website.

bioconductor.org/packages/devel/bioc/html/epihet.html

but, I checked bioconductor.org/checkResults/devel/bioc-LATEST/epihet/ again today, why it told me build is wrong. I am confused.

Best,
Xiaowen

On 11/20/20, 1:00 PM, "BBS-noreply using bioconductor.org" <BBS-noreply using bioconductor.org> wrote:

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

    Hi epihet maintainer,

    According to the Multiple platform build/check report for BioC 3.12,
    the epihet package has the following problem(s):

      o ERROR for 'R CMD build' on malbec1. See the details here:
          https://secure-web.cisco.com/1fRXgUrwUkGrlrUDBrAssYtjnWZ-Ei1qmcSwfCkNOpPfQsZvTKlMKAUwIM0Ag_-qE1zFpBvCdNihAlCt6_fYWYphCHVxFB5wyxcQqR0gzMNayDOvQwTmufIBoA8d2RwGmEFUvgggpZAVFxwNP0Zbu_89smQJZwjII5_ag8UQkhFvdtphCVpQfyHdDVfUMGS-Rm24LeQn3HMPHMMGV6yy4Eov__WPpc-wmnktd6BeAnZ4bUWfezkpiFvyqLcwiq_9noR4g9avJtIL8Nnx9OPq7KkClUOvoOsgkAerycbIhZ0iraZJYEcV9qF3Zi8-Q-lxf/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.12%2Fbioc-LATEST%2Fepihet%2Fmalbec1-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
        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.

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