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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:piano.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings piano_2.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/piano.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘piano/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘piano’ version ‘2.21.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘piano’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘piano-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: networkPlot2
> ### Title: Gene set network plot
> ### Aliases: networkPlot2
> 
> ### ** Examples
> 
> 
>    # Load example input data to GSA:
>    data("gsa_input")
>    
>    # Load gene set collection:
>    gsc <- loadGSC(gsa_input$gsc)
>       
>    # Run gene set analysis:
>    gsares <- runGSA(geneLevelStats=gsa_input$pvals , directions=gsa_input$directions, 
+                     gsc=gsc, nPerm=500)
Running gene set analysis:
Checking arguments...done!
Final gene/gene-set association: 1136 genes and 50 gene sets
  Details:
  Calculating gene set statistics from 1136 out of 2000 gene-level statistics
  Using all 2000 gene-level statistics for significance estimation
  Removed 0 genes from GSC due to lack of matching gene statistics
  Removed 0 gene sets containing no genes after gene removal
  Removed additionally 0 gene sets not matching the size limits
  Loaded additional information for 0 gene sets
Calculating gene set statistics...done!
Calculating gene set significance...done!
Adjusting for multiple testing...done!
>       
>    # Network plot:
>    networkPlot2(gsares, class="non", significance=0.1)
Warning in dir.create(target_dir) :
  cannot create dir 'lib/visNetwork-binding-2.1.2', reason 'No space left on device'
Error in normalizePath(target_dir, "/", TRUE) : 
  path[1]="lib/visNetwork-binding-2.1.2": No such file or directory
Calls: <Anonymous> ... lapply -> FUN -> copyDependencyToDir -> normalizePath
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘Running_gene-set_analysis_with_piano.Rmd’ using rmarkdown
--- finished re-building ‘Running_gene-set_analysis_with_piano.Rmd’

--- re-building ‘piano-vignette.Rnw’ using Sweave
Loading data in text file...
...done
Loading setup file...
...done
Text file data: No normalization performed.

Creating annotation...
...done
Removing unmapped probes...
..done
Warning in runQC(myArrayData) :
  can not run rnaDeg: argument arrayData does not contain dataRaw
Warning in runQC(myArrayData) :
  can not run nuseRle: argument arrayData does not contain dataRaw
Generating normalized data distribution plot...
...done
Generating normalized data boxplot...
dev.new(): using pdf(file="Rplots1.pdf")
...done
Generating PCA...
...done
dev.new(): using pdf(file="Rplots2.pdf")
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
Generating PCA...
...done
dev.new(): using pdf(file="Rplots6.pdf")
dev.new(): using pdf(file="Rplots7.pdf")
dev.new(): using pdf(file="Rplots8.pdf")
dev.new(): using pdf(file="Rplots9.pdf")
Generating PCA...
...done
dev.new(): using pdf(file="Rplots10.pdf")
dev.new(): using pdf(file="Rplots11.pdf")
dev.new(): using pdf(file="Rplots12.pdf")
dev.new(): using pdf(file="Rplots13.pdf")
Warning in plot.new() :
  Cannot open temporary file '/tmp/Rtmpc1iJs2/pdf1e2beb13e8d932' for compression (reason: No space left on device); compression has been turned off for this device
Warning in file() :
  cannot open file '/tmp/Rtmpc1iJs2/Rf1e2beb5b946ceb': No space left on device
Error: processing vignette 'piano-vignette.Rnw' failed with diagnostics:
cannot open the connection
--- failed re-building ‘piano-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘piano-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Converting parsed Rd's to LaTeX ..
Creating pdf output from LaTeX ...
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex)
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\T1/ptm/m/n/10 Leif Varemo Wigge \T1/pcr/m/n/10 <piano.rpkg@gmail.com> \T1/ptm/
m/n/10 and Intawat Nookaew \T1/pcr/m/n/10 <piano.rpkg@gmail.com>  
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\T1/ptm/m/n/10 and the cen-tral func-tion for this is [][][]\T1/pcr/m/n/10 runG
SA[][][]\T1/ptm/m/n/10 . There are some down-stream func-tions (e.g. [][][]\T1/
pcr/m/n/10 GSAsummaryTable[][]

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[]\T1/ptm/m/n/10 Leif Varemo \T1/pcr/m/n/10 <piano.rpkg@gmail.com> \T1/ptm/m/n/
10 and Intawat Nookaew \T1/pcr/m/n/10 <piano.rpkg@gmail.com> 
[2]
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[]\T1/ptm/m/n/10 Leif Varemo \T1/pcr/m/n/10 <piano.rpkg@gmail.com> \T1/ptm/m/n/
10 and Intawat Nookaew \T1/pcr/m/n/10 <piano.rpkg@gmail.com> 
[3]
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\T1/ptm/m/n/10 should be used as sig-nif-i-cance in-for-ma-tion for the plot. C
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[4]
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[]\T1/ptm/m/n/10 a char-ac-ter string se-lect-ing the method, ei-ther "mean", "
me-dian", "max", "Borda"

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[]\T1/ptm/m/n/10 Leif Varemo \T1/pcr/m/n/10 <piano.rpkg@gmail.com> \T1/ptm/m/n/
10 and Intawat Nookaew \T1/pcr/m/n/10 <piano.rpkg@gmail.com> 
[5]
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 []   \T1/pcr/m/n/9 # Consensus scores for the top 50 gene sets (in the non-dir
ectional class):[] 

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 []  \T1/pcr/m/n/10 colors = c("red", "green", "blue", "yellow", "orange", "pur
ple", "tan", "cyan",[] 

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\T1/ptm/m/n/10 be []\T1/pcr/m/n/10 "holm"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "h
ochberg"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "hommel"[]\T1/ptm/m/n/10 , []\T1/pc
r/m/n/10 "bonferroni"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "BH"[]\T1/ptm/m/n/10 ,
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[6]
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 []\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 m1\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/
pcr/m/n/10 '\T1/pcr/m/n/10 m2\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 compared to \TS1/
pcr/m/n/10 '\T1/pcr/m/n/10 wt\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 : diffExp(arrayDat
a, contrasts=c("m1 - wt",[] 

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[]\T1/pcr/m/n/10 data.frame []\T1/ptm/m/n/10 con-tain-ing ad-justed p-values (a
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[7]
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[]\T1/ptm/m/n/10 Leif Varemo \T1/pcr/m/n/10 <piano.rpkg@gmail.com> \T1/ptm/m/n/
10 and Intawat Nookaew \T1/pcr/m/n/10 <piano.rpkg@gmail.com> 

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 []  \T1/pcr/m/n/9 myArrayData <- loadMAdata(datadir=dataPath, dataNorm="norm_d
ata.txt.gz", platform="yeast2")[] 

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 []  \T1/pcr/m/n/9 pfc <- diffExp(myArrayData, contrasts=c("aerobic_Clim - anae
robic_Clim",[] 

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 []                                          \T1/pcr/m/n/9 "aerobic_Nlim - anae
robic_Nlim"))[] 

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 []  \T1/pcr/m/n/9 # Order the genes according to p-values, for aerobic_Clim vs
 anaerobic_Clim:[] 
[8]
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 []   \T1/pcr/m/n/9 gsares <- runGSA(geneLevelStats=gsa_input$pvals , direction
s=gsa_input$directions,[] 
[9]
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 []  \T1/pcr/m/n/9 myArrayData <- loadMAdata(datadir=dataPath, dataNorm="norm_d
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[10]
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 []   \T1/pcr/m/n/9 gsares <- runGSA(geneLevelStats=gsa_input$pvals , direction
s=gsa_input$directions,[] 
[11]
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[]\T1/ptm/m/n/10 Leif Varemo \T1/pcr/m/n/10 <piano.rpkg@gmail.com> \T1/ptm/m/n/
10 and Intawat Nookaew \T1/pcr/m/n/10 <piano.rpkg@gmail.com> 
[12
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(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
(./Rd2.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (./Rd2.out) (./Rd2.out
! I can't write on file `Rd2.pdf'.
(Press Enter to retry, or Control-D to exit; default file extension is `.pdf')
Please type another file name for output
! Emergency stop.
\Hy@OutlineName ...utline goto name{#2}count#3{#4}
                                                  
l.1 ...\000-\000p\000a\000c\000k\000a\000g\000e}{}
                                                  % 1
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on Rd2.log.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  unable to run pdflatex on 'Rd2.tex'
LaTeX errors:
! I can't write on file `Rd2.pdf'.
(Press Enter to retry, or Control-D to exit; default file extension is `.pdf')
Please type another file name for output
! Emergency stop.
! Emergency stop.
\Hy@OutlineName ...utline goto name{#2}count#3{#4}
                                                  
l.1 ...\000-\000p\000a\000c\000k\000a\000g\000e}{}
                                                  % 1
!  ==> Fatal error occurred, no output PDF file produced!
Error in running tools::texi2pdf()
You may want to clean up by 'rm -Rf /tmp/RtmpZe3zoX/Rd2pdf1dd2235b1cd4c8'
* DONE

Status: 3 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/piano.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL piano
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘piano’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (piano)