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### Running command:
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###   chmod a+r GGPA -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GGPA
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* checking for file 'GGPA/DESCRIPTION' ... OK
* preparing 'GGPA':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'GGPA-example.Rnw' using Sweave
Loading required package: GGally
Loading required package: ggplot2
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
Loading required package: network

'network' 1.19.0 (2024-12-08), part of the Statnet Project
* 'news(package="network")' for changes since last version
* 'citation("network")' for citation information
* 'https://statnet.org' for help, support, and other information

Loading required package: sna
Loading required package: statnet.common

Attaching package: 'statnet.common'

The following objects are masked from 'package:base':

    attr, order

sna: Tools for Social Network Analysis
Version 2.8 created on 2024-09-07.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.

Loading required package: scales
Loading required package: matrixStats
Warning in plot.window(...) : "size" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "size" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "size" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "size" is not a graphical parameter
Warning in box(...) : "size" is not a graphical parameter
Warning in title(...) : "size" is not a graphical parameter
Info: Uniform prior will be used for the phenotype graph in the estimation.
Info: Number of GWAS data: 7
Info: Some SNPs have p-values close to zero.
Info: Number of SNPs with p-values close to zero: 234
Info: p-values for these SNPs are set to 1e-10

Burn in iterations...

Burn-in iteration: 100 / 200
The last 100 iter= 0.1 min, Est. Time to go= 0.1 min
Burn-in iteration: 200 / 200
The last 100 iter= 0.1 min, Est. Time to go= 0 min

Main MCMC iterations...

Burn-in iteration: 100 / 200
The last 100 iter= 0.1 min, Est. Time to go= 0.1 min
Burn-in iteration: 200 / 200
The last 100 iter= 0.2 min, Est. Time to go= 0 min
Info: Association mapping for each phenotype.
Info: Association mapping based on the global FDR control at level 0.1.
Info: Association mapping for specified i & j phenotype pair.
Info: Association mapping based on the global FDR control at level 0.1.
Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 1033
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "GGPA-example.tex" ' had status 1033
Error: processing vignette 'GGPA-example.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'GGPA-example.pdf' for vignette with name 'GGPA-example' and engine 'utils::Sweave'. The following files exist in working directory 'E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpueyXan\Rbuildc1c47d231982\GGPA\vignettes': 'GGPA-example-concordance.tex' (377 bytes), 'GGPA-example-fig-pgraph.pdf' (4585 bytes), 'GGPA-example.Rnw' (13477 bytes), 'GGPA-example.tex' (16886 bytes), 'ddnet_step1.png' (706725 bytes), 'ddnet_step2.png' (785600 bytes), 'ddnet_step3.png' (437776 bytes), 'ddnet_step4.png' (386838 bytes)
--- failed re-building 'GGPA-example.Rnw'

SUMMARY: processing the following file failed:
  'GGPA-example.Rnw'

Error: Vignette re-building failed.
Execution halted