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

Martin Morgan 
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 at r-project.org on behalf of Xiaowen.Chen at 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 at RoswellPark.org>
    Date: Monday, November 23, 2020 at 4:05 PM
    To: Xiaowen Chen <Xiaowen.Chen at jax.org>
    Cc: "bioc-devel at r-project.org" <bioc-devel at 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 at git.bioconductor.org:packages/epihet.git


    (base) shepherd at 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

Thread (9 messages)

Xiaowen Chen epihet problems reported in the Multiple platform build/check report for BioC 3.12 Nov 23 Shepherd, Lori epihet problems reported in the Multiple platform build/check report for BioC 3.12 Nov 23 Xiaowen Chen epihet problems reported in the Multiple platform build/check report for BioC 3.12 Nov 23 Shepherd, Lori epihet problems reported in the Multiple platform build/check report for BioC 3.12 Nov 23 Shepherd, Lori epihet problems reported in the Multiple platform build/check report for BioC 3.12 Nov 23 Xiaowen Chen epihet problems reported in the Multiple platform build/check report for BioC 3.12 Nov 24 Martin Morgan epihet problems reported in the Multiple platform build/check report for BioC 3.12 Nov 24 Xiaowen Chen epihet problems reported in the Multiple platform build/check report for BioC 3.12 Nov 24 Martin Morgan epihet problems reported in the Multiple platform build/check report for BioC 3.12 Nov 24