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-boun...@r-project.org> on behalf of Christopher
John <chris.r.joh...@gmail.com>
Sent: Monday, November 11, 2019 6:15 AM
To: bioc-devel@r-project.org <bioc-devel@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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