[Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12
Martin Morgan
mtmorg@n@b|oc @end|ng |rom gm@||@com
Tue Nov 24 22:43:59 CET 2020
not sure that this is a good answer or not, but on scanning your vignette I didn't see any use of LaTeX math expressions, so perhaps mathptmx is not needed at all in and can be removed from the vignette?
At any rate when I remove it and try
epihet/vignettes master$ R CMD Sweave --pdf epihet.Rnw
using R with the correct version (BiocManager::version() returns 3.13) and valid package installation (BiocManager::valid() returns TRUE) I get
'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 483-495 (/Users/ma38727/b/git/epihet/vignettes/epihet.Rnw)
Error in ans[ypos] <- rep(yes, length.out = len)[ypos] :
replacement has length zero
Calls: <Anonymous> ... expand_limits_discrete_trans -> expand_limits_continuous_trans -> ifelse
Execution halted
which is the same as the build system, and occurs before the LaTeX processing step and so does not require that mathptmx be installed to troubleshoot this error...
Martin
On 11/24/20, 3:39 PM, "Bioc-devel on behalf of Xiaowen Chen" <bioc-devel-bounces using r-project.org on behalf of Xiaowen.Chen using jax.org> wrote:
Hi Kern,
I followed your suggestion and updated my Bioconductor version and epihet,
Then when I build epihet, it complained that
The following object is masked from 'package:clusterProfiler':
select
'select()' returned 1:1 mapping between keys and columns
Error: processing vignette 'epihet.Rnw' failed with diagnostics:
pdflatex is not available
--- failed re-building ‘epihet.Rnw’
SUMMARY: processing the following file failed:
‘epihet.Rnw’
Error: Vignette re-building failed.
I check my HPC has not pdflatex, so I installed tinytex from the website https://yihui.org/tinytex/ using following command lines:
remotes::install_github('yihui/tinytex')
tinytex::install_tinytex()
but another error occurred :
Error: processing vignette 'epihet.Rnw' failed with diagnostics:
unable to run pdflatex on 'epihet.tex'
LaTeX errors:
! LaTeX Error: File `mathptmx.sty' not found.
I tried it :
tlmgr install mathptmx.sty
tlmgr: package repository http://ctan.mirrors.hoobly.com/systems/texlive/tlnet (verified)
tlmgr install: package mathptmx.sty not present in repository.
tlmgr: action install returned an error; continuing.
tlmgr: An error has occurred. See above messages. Exiting.
Could you give me some suggestions?
Thank you!
Best,
Xiaowen
From: "Kern, Lori" <Lori.Shepherd using RoswellPark.org>
Date: Monday, November 23, 2020 at 4:05 PM
To: Xiaowen Chen <Xiaowen.Chen using jax.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
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<https://secure-web.cisco.com/13ME5udh0lLv3ehK1PeyOyLO9xbkTKwCqHl8jAsHeIglZuTNEiWMoKrgyxkIs33gOZSmv9yEJhhph2bxvCuZUziL1myywPP5rPGNeXanPTQaCLrtCCJegdoAlXOvbRQtpz8qfYM3zqusEd8tE2LMAJ6EeB5fc-WK9PFoZ4rOGPf4X6B351ytCsh1D85fwJ33IBUTItGSuV0TuTA0z0fA1vADO3dUBkpH-nExIFPq_0ywcMg92NkxDIAIiWH4YsfV6ZvorH-6yclcytvPeZng2uDkTLKUITmxIW0juDcMp1uisZ4CuqDt-Dg-XckrOIklu/https%3A%2F%2Fgithub.com%2FTheJacksonLaboratory%2Fepihet.git%3chttps:/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
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