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

Mon Nov 23 22:05:01 CET 2020

And For What Its Worth -  I can reproduce the ERROR locally using a git clone from
git using git.bioconductor.org:packages/epihet.git

(base) shepherd using jbcj433:~/BioconductorPackages/Software$ R CMD build epihet
Bioconductor version 3.13 (BiocManager 1.30.10), ?BiocManager::install for help
* checking for file 'epihet/DESCRIPTION' ... OK
* preparing 'epihet':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘epihet.Rnw’ using knitr
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: 'AnnotationDbi'

The following object is masked from 'package:clusterProfiler':

    select

'select()' returned 1:1 mapping between keys and columns
Warning in rep(yes, length.out = len) :
  'x' is NULL so the result will be NULL
Quitting from lines 484-496 (epihet.Rnw)
Error: processing vignette 'epihet.Rnw' failed with diagnostics:
replacement has length zero
--- failed re-building ‘epihet.Rnw’

SUMMARY: processing the following file failed:
  ‘epihet.Rnw’

Error: Vignette re-building failed.
Execution halted

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 Kern, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Monday, November 23, 2020 4:01 PM
To: Xiaowen Chen <Xiaowen.Chen using jax.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

Please make sure your github repositories are up-to-date with the git.bioconductor.org repositories.  On quick glance, I can see you have not pulled the changes on the bioconductor server since the version numbers are not up-to-date for relesae and devel.  The version we have at git.bioconductor.org is the version of the package we are building and checking. not a github repository.  Perhaps you forgot to push changes to the git.bioconductor.org repository?
I suggest you check out the git help pages especially for

Syncing with Bioconductor:
http://secure-web.cisco.com/1_ed4MO3wzGEv9vtahMGt3EjH_fRdxuy-Ggwfv072LHMg33gJDq6NJ-O4j8ElxPP6icz-SAKtYbg7YAb7NdXVsKWMH8rsoXdimZDOKZDL7d1c-Mb6cggFxH5YKCjkmj08UrH5at6XPatjaa6_LPY4cOVXz-hkOZCdt7p7octVbhxBusXEUQExxebo1-rsrzBqvFppOI8qnlYv5hosKQk6izKY5rjKG_JhkfAIfazaOWJBSZXxxE9Ml4V8YhYZOEZXt470d1XSlY8F-lsYsPTTiaLRveK0RbPuwODtpKAm609JGxKZmcpOUNeXoX8TTLMg/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F

Pushing to Bioconductor release and devel:
http://secure-web.cisco.com/1Xg3LpZwFnSWhmcDJ_Cyy7XvU1VQn3SiYLwUSqjNAoFWlNnuYj0VmoRb53jBGHdlG73IPrxMQlsLZyP0hBmOi9kVhS2yTbZMs5OWxmyWWW-6f_i_lklGJ5LmzPDeW7bYBmZ4NqRPdQenUdQ460VyVO9wcXxyHHv0wpPEs8YAV4BlRDIXRA7Y6QeuDZbInXsw0YnL0ba7Swify49bnp-OyHs4gvC8p11paPMo_w07Zk0dbcexLbs9reMtR-lWRvGV9NGtSycUHQNNZlkYay03mW_eCIAthyAYaaxxFYg8GBD1srNlOD8qKFcL954Spxjp_/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F

Other things to consider:

Make sure you are using the latest version of R and that all package dependencies are up to date.

For Release you should be using R 4.0.3 with Bioconductor 3.12.  Make sure all packages are up-to-date by running
BiocManager::install(version="3.12")
BiocManager::valid()   and/or   BiocManager::install()

For Devel you should be using R-devel  (what will be  R 4.1.0)  and Bioconductor 3.13. Again make sure packages are updated for this version
BiocManager::install(version="devel")
BiocManager::valid()   and/or   BiocManager::install()

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Xiaowen Chen <Xiaowen.Chen using jax.org>
Sent: Monday, November 23, 2020 3:29 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: 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

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://secure-web.cisco.com/13ME5udh0lLv3ehK1PeyOyLO9xbkTKwCqHl8jAsHeIglZuTNEiWMoKrgyxkIs33gOZSmv9yEJhhph2bxvCuZUziL1myywPP5rPGNeXanPTQaCLrtCCJegdoAlXOvbRQtpz8qfYM3zqusEd8tE2LMAJ6EeB5fc-WK9PFoZ4rOGPf4X6B351ytCsh1D85fwJ33IBUTItGSuV0TuTA0z0fA1vADO3dUBkpH-nExIFPq_0ywcMg92NkxDIAIiWH4YsfV6ZvorH-6yclcytvPeZng2uDkTLKUITmxIW0juDcMp1uisZ4CuqDt-Dg-XckrOIklu/https%3A%2F%2Fgithub.com%2FTheJacksonLaboratory%2Fepihet.git<https://secure-web.cisco.com/1V1wbCFIhxFhA5kUBA3jrA7KJagNvphSlVg9vE3cipv5RZPIj_pYe8DiUKSpfqZYu3HfCWgeMvtjHHzkkA7TqrPyiyJZFybwaSVcQOGaOPs4WSE5n0FdpxzD7cH-Gmy_CDlYONl1N_p-VBf4W9Y1YiB47umcZaUSxEeDhoK3nwP8Lj393X05hzzjXyMJoGpUlTI2LXtc3VB7sWP68xEZ6Yj7ZxPsG3k9pjTM3UX9RDLKoEavuj0wVhumf9hpCOaagZeYbx19-JLVAb4OD2fMTGC6ZNJ61z8LhLkEsOQsHIhHMSRssvT_hNAmmcYBdW1fc/https%3A%2F%2Fgithub.com%2FTheJacksonLaboratory%2Fepihet.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.

      * If you have questions about this report or need help with the
        maintenance of your package, please use the Bioc-devel mailing list:

          https://secure-web.cisco.com/1_7E5OlJQt1L6CDez_cje5Rll39xYbr1dzA_gY80oK0T7QPCCw_NrsmbHec-DGJbKBlUO-Icx-P31S8j3TV_kxeXELPzefr_cBmzKwXYr_TvNrZXPFutuo_wS2tVkJDEcxkg7ZipWs3dgY6yV9ugTXRwRguB99b3KcbIp--5TObxzeqj-T8IqbUjmb8Hs6xAIi5Mx8FXFQQh60dH8sqY9t8ShzQBWigMKt106ZKCkpKsC3nWTDV7VSQhn46Cdxmvd4qIvXE2KXw20DHwogf2icebqNZ1yUi97isFnSSoTQoJBTNXWEXRQzvOyu-o2Y1Gn/https%3A%2F%2Fbioconductor.org%2Fhelp%2Fmailing-list%2F

        (all package maintainers are requested to subscribe to this list)

    For immediate notification of package build status, please
    subscribe to your package's RSS feed. Information is at:

    https://secure-web.cisco.com/1jJfXEOikiiqfVUMXXXYLgOH3PtOEakho4YndnURyzvA3uocma-aT_0lLkvkeVGP8C6LOIxwrySxqxNUW9EWTyBwQ4YyKvFgOs7-KJjEU_uQpXf-IwKKf4jjY-Zs1AwNOJZDsjleA6e2-kBK2WQSapc3MrI7vGJd6P51g7f10l7fGyFPhwXUPnIAjFHKvvv-SpbXpyGRoKnctCajNMyvq1WlCQUCUozixQD5FRMq1lWm5qiGJnRNc5M65pKfnxqwbJcVXbSBfa3QmhRiLmFPEFIsRo7U35iSPdfjoawRdP98EA95zoVXGTRfcVWuWhFxS/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Frss-feeds%2F

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