[Bioc-devel] New error appeared on dev without updating the development version

[Shepherd, Lori]

We haven't forgotten about this and are looking into it. We hope to report back with more information soon.


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 Christopher John <chris.r.john86 using gmail.com>
Sent: Monday, November 11, 2019 6:15 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] New error appeared on dev without updating the development version

Hi

I haven't done an update in a while, but got the following error message
like yesterday just on windows, any ideas? Seems vignette related. Thanks.

Chris

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r M3C -R && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe
CMD build --keep-empty-dirs --no-resave-data M3C
###
##############################################################################
##############################################################################


* checking for file 'M3C/DESCRIPTION' ... OK
* preparing 'M3C':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'M3Cvignette.Rmd' using rmarkdown
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

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

    isFALSE

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO:
windows] | Cores 39/40

Attaching package: 'gplots'

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

    lowess

***PCA wrapper function***
running...
done.
***M3C***
method: Monte Carlo simulation
clustering algorithm: pam
annotation: yes
running simulations...
done.
running consensus cluster algorithm for real data...
done.
running clinical analysis type: chi
optimal K: 4
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-7-1.pdf'.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-8-1.pdf'.
***PCA wrapper function***
running...
done.
***t-SNE wrapper function***
running...
done.
***M3C***
method: penalised stability
clustering algorithm: pam
annotation: none
running consensus cluster algorithm for real data...
done.
optimal K: 5
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-10-1.pdf'.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-10-2.pdf'.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-10-3.pdf'.
***clustersim***
computing simulated data using linear combination...
calculating PCs of data and performing kmeans...
computing centroids of clusters and pulling apart...
transforming pulled apart PC co ordinates back to dataset...
finished.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-11-1.pdf'.
! Package ifvtex Error: Name clash, \ifvtex is already defined.

Error: processing vignette 'M3Cvignette.Rmd' failed with diagnostics:
Failed to compile M3Cvignette.tex. See
https://yihui.name/tinytex/r/#debugging for debugging tips. See
M3Cvignette.log for more info.
--- failed re-building 'M3Cvignette.Rmd'

SUMMARY: processing the following file failed:
  'M3Cvignette.Rmd'

Error: Vignette re-building failed.
Execution halted

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