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

Xiaowen Chen 
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