##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cellHTS2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings cellHTS2_2.63.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/cellHTS2.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘cellHTS2/DESCRIPTION’ ... OK
* this is package ‘cellHTS2’ version ‘2.63.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'RColorBrewer', 'Biobase', 'genefilter', 'splots', 'vsn', 'hwriter',
  'locfit', 'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cellHTS2’ 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 R 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘genefilter’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘Biobase:::.showAnnotatedDataFrame’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotPlate: no visible global function definition for ‘dev.cur’
plotPlate: no visible global function definition for ‘plot.new’
Undefined global functions or variables:
  dev.cur plot.new
Consider adding
  importFrom("grDevices", "dev.cur")
  importFrom("graphics", "plot.new")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown packages ‘cellHTS’, ‘prada’ in Rd xrefs
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘cellhts2.Rnw’... OK
  ‘cellhts2Complete.Rnw’... failed
  ‘twoChannels.Rnw’... OK
  ‘twoWay.Rnw’... OK
 WARNING
Errors in running code in vignettes:
when running code in ‘cellhts2Complete.Rnw’
  ...
> categs <- cateGOry(genes, unlist(goids, use.names = FALSE))
Loading required namespace: GO.db
Failed with error:  ‘there is no package called ‘GO.db’’

  When sourcing ‘cellhts2Complete.R’:
Error: Use 'BiocManager::install("GO.db")' to install the GO.db package
recover called non-interactively; frames dumped, use debugger() to view
> proc.time()
   user  system elapsed 
 19.629   0.687  20.232 

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘cellhts2.Rnw’ using Sweave
Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages
    'citation("pkgname")'.

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.7 	 2023-01-02
Loading required package: grid
Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument.
We recommend storing this script for future reference along with the report.
Warning in sprintf("Left: raw, right: normalized", r) :
  one argument not used by format 'Left: raw, right: normalized'
Warning in sprintf("Left: raw, right: normalized", r) :
  one argument not used by format 'Left: raw, right: normalized'
Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument.
We recommend storing this script for future reference along with the report.
Warning: `qplot()` was deprecated in ggplot2 3.4.0.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 24 rows containing non-finite values (`stat_bin()`).
Warning: Removed 446 rows containing non-finite values (`stat_binhex()`).
Warning: Computation failed in `stat_binhex()`
Caused by error in `compute_group()`:
! The package "hexbin" is required for `stat_binhex()`
Warning: Removed 24 rows containing non-finite values (`stat_qq()`).
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 24 rows containing non-finite values (`stat_bin()`).
Warning: Removed 502 rows containing non-finite values (`stat_binhex()`).
Warning: Computation failed in `stat_binhex()`
Caused by error in `compute_group()`:
! The package "hexbin" is required for `stat_binhex()`
Warning: Removed 24 rows containing non-finite values (`stat_qq()`).
--- finished re-building ‘cellhts2.Rnw’

--- re-building ‘cellhts2Complete.Rnw’ using Sweave
Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages
    'citation("pkgname")'.

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.7 	 2023-01-02
Loading required package: grid
Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument.
We recommend storing this script for future reference along with the report.
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: Matrix

Attaching package: ‘Matrix’

The following object is masked from ‘package:S4Vectors’:

    expand

Loading required namespace: GO.db
Failed with error:  ‘there is no package called ‘GO.db’’

Error: processing vignette 'cellhts2Complete.Rnw' failed with diagnostics:
 chunk 40 (label = cat1) 
Error in augmentByAncestors(ux) : 
  Use 'BiocManager::install("GO.db")' to install the GO.db package

--- failed re-building ‘cellhts2Complete.Rnw’

--- re-building ‘twoChannels.Rnw’ using Sweave
Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.7 	 2023-01-02
Loading required package: grid
Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument.
We recommend storing this script for future reference along with the report.
Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument.
We recommend storing this script for future reference along with the report.
--- finished re-building ‘twoChannels.Rnw’

--- re-building ‘twoWay.Rnw’ using Sweave
Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.7 	 2023-01-02
Loading required package: grid
Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument.
We recommend storing this script for future reference along with the report.
Warning in sprintf("Left: raw, right: normalized", r) :
  one argument not used by format 'Left: raw, right: normalized'
Warning in sprintf("Left: raw, right: normalized", r) :
  one argument not used by format 'Left: raw, right: normalized'
Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument.
We recommend storing this script for future reference along with the report.
--- finished re-building ‘twoWay.Rnw’

SUMMARY: processing the following file failed:
  ‘cellhts2Complete.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/cellHTS2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL cellHTS2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘cellHTS2’ ...
** 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 (cellHTS2)

R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ## cat tests/test.R | R --vanilla
> ## cellHTS2 crash test on various conditions
> library(cellHTS2)
Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.7 	 2023-01-02
Loading required package: grid
> path <- system.file("testscreen", package="cellHTS2")
> 
> testPlatelist=function(platelist, normalize=TRUE)
+ {
+     x <- readPlateList(platelist, name="test", path=path)
+     x <- configure(x, descripFile="description.txt", confFile="plateconf.txt",
+                    logFile="screenlog.txt", path=path)
+     
+     if (normalize)
+     {
+         ## normalize results
+         xn <- normalizePlates(x, scale="multiplicative", log=FALSE, method="median",
+                               varianceAdjust="none")
+         
+         ## score and summarize replicates
+         xsc <- scoreReplicates(xn, sign="-", method="zscore")
+         xsc <- summarizeReplicates(xsc, summary="mean")
+     }
+     
+     ## write reports
+     outdir <- file.path(tempdir(),platelist,'raw')
+     mainScriptFile <-  system.file("scripts/dummy.R", package="cellHTS2")
+     writeReport(raw=x, force=TRUE, plotPlateArgs = TRUE,imageScreenArgs = list(zrange=c( -4, 8), ar=1),
+                 map=TRUE, outdir=outdir, mainScriptFile=mainScriptFile)
+     if (interactive()) browseURL(file.path(outdir,'index.html'))
+     if (normalize)
+     {
+         outdir <- file.path(tempdir(),platelist,'norm')
+         writeReport(raw=x, normalized=xn, scored=xsc, force=TRUE, plotPlateArgs = TRUE,
+                     imageScreenArgs = list(zrange=c( -4, 8), ar=1), map=TRUE, outdir=outdir,
+                     mainScriptFile=mainScriptFile)
+         if (interactive()) browseURL(file.path(outdir,'index.html'))
+     }
+ }
> 
> ######
> ## 2 plates, 2 replicates, 1 channel
> testPlatelist('platelist221.txt')
cellHTS2 is busy creating HTML pages for 'test'. 
Found raw data.
State:
configured=TRUE, annotated=FALSE

0% done (step 1 of 6)
33% done (step 2 of 6)
38% done (step 3 of 6)
42% done (step 3 of 6)
52% done (step 4 of 6)
88% done (step 5 of 6)
100% done (step 5 of 6)
100% done (step 5 of 6)
100% done (step 6 of 6)
Report was successfully generated in folder /tmp/RtmpDFrBX1/platelist221.txt/raw/index.html
cellHTS2 is busy creating HTML pages for 'test'. 
Found raw, normalized and scored data.
State:
configured=TRUE, annotated=FALSE

0% done (step 1 of 8)
17% done (step 2 of 8)
19% done (step 3 of 8)
22% done (step 3 of 8)
27% done (step 4 of 8)
46% done (step 5 of 8)
92% done (step 6 of 8)
94% done (step 7 of 8)
100% done (step 8 of 8)
Report was successfully generated in folder /tmp/RtmpDFrBX1/platelist221.txt/norm/index.html
Warning messages:
1: The plotPlateArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
2: The imageScreenArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
3: The plotPlateArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
4: The imageScreenArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
5: In sprintf("Left: raw, right: normalized", r) :
  one argument not used by format 'Left: raw, right: normalized'
6: In sprintf("Left: raw, right: normalized", r) :
  one argument not used by format 'Left: raw, right: normalized'
> 
> ######
> ## 2 plates, 1 replicate, 2 channels
> testPlatelist('platelist212.txt', normalize=FALSE)
cellHTS2 is busy creating HTML pages for 'test'. 
Found raw data.
State:
configured=TRUE, annotated=FALSE

0% done (step 1 of 6)
33% done (step 2 of 6)
38% done (step 3 of 6)
42% done (step 3 of 6)
52% done (step 4 of 6)
88% done (step 5 of 6)
100% done (step 5 of 6)
100% done (step 5 of 6)
100% done (step 6 of 6)
Report was successfully generated in folder /tmp/RtmpDFrBX1/platelist212.txt/raw/index.html
Warning messages:
1: The plotPlateArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
2: The imageScreenArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
> 
> ######
> ## 2 plates, 1 replicate, 3 channels
> testPlatelist('platelist213.txt', normalize=FALSE)
cellHTS2 is busy creating HTML pages for 'test'. 
Found raw data.
State:
configured=TRUE, annotated=FALSE

0% done (step 1 of 6)
26% done (step 2 of 6)
31% done (step 3 of 6)
37% done (step 3 of 6)
48% done (step 4 of 6)
91% done (step 5 of 6)
100% done (step 5 of 6)
100% done (step 5 of 6)
100% done (step 6 of 6)
Report was successfully generated in folder /tmp/RtmpDFrBX1/platelist213.txt/raw/index.html
Warning messages:
1: The plotPlateArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
2: The imageScreenArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
> 
> ######
> ## 2 plates, 2 replicates, 2 channels
> testPlatelist('platelist222.txt', normalize=FALSE)
cellHTS2 is busy creating HTML pages for 'test'. 
Found raw data.
State:
configured=TRUE, annotated=FALSE

0% done (step 1 of 6)
21% done (step 2 of 6)
27% done (step 3 of 6)
33% done (step 3 of 6)
46% done (step 4 of 6)
92% done (step 5 of 6)
100% done (step 5 of 6)
100% done (step 5 of 6)
100% done (step 6 of 6)
Report was successfully generated in folder /tmp/RtmpDFrBX1/platelist222.txt/raw/index.html
Warning messages:
1: The plotPlateArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
2: The imageScreenArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
> 
> ######
> ## 2 plates, 1 replicates, 1 channel
> testPlatelist('platelist211.txt')
cellHTS2 is busy creating HTML pages for 'test'. 
Found raw data.
State:
configured=TRUE, annotated=FALSE

0% done (step 1 of 6)
46% done (step 2 of 6)
49% done (step 3 of 6)
52% done (step 3 of 6)
59% done (step 4 of 6)
84% done (step 5 of 6)
100% done (step 5 of 6)
100% done (step 5 of 6)
100% done (step 6 of 6)
Report was successfully generated in folder /tmp/RtmpDFrBX1/platelist211.txt/raw/index.html
cellHTS2 is busy creating HTML pages for 'test'. 
Found raw, normalized and scored data.
State:
configured=TRUE, annotated=FALSE

0% done (step 1 of 8)
28% done (step 2 of 8)
30% done (step 3 of 8)
31% done (step 3 of 8)
36% done (step 4 of 8)
51% done (step 5 of 8)
88% done (step 6 of 8)
90% done (step 7 of 8)
100% done (step 8 of 8)
Report was successfully generated in folder /tmp/RtmpDFrBX1/platelist211.txt/norm/index.html
Warning messages:
1: The plotPlateArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
2: The imageScreenArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
3: The plotPlateArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
4: The imageScreenArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
5: In sprintf("Left: raw, right: normalized", r) :
  one argument not used by format 'Left: raw, right: normalized'
> 
> ######
> ## 2 plates, 3 replicates, 3 channels
> testPlatelist('platelist233.txt', normalize=FALSE)
cellHTS2 is busy creating HTML pages for 'test'. 
Found raw data.
State:
configured=TRUE, annotated=FALSE

0% done (step 1 of 6)
11% done (step 2 of 6)
18% done (step 3 of 6)
25% done (step 3 of 6)
40% done (step 4 of 6)
96% done (step 5 of 6)
100% done (step 5 of 6)
100% done (step 5 of 6)
100% done (step 6 of 6)
Report was successfully generated in folder /tmp/RtmpDFrBX1/platelist233.txt/raw/index.html
Warning messages:
1: The plotPlateArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
2: The imageScreenArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'. 
> 
> proc.time()
   user  system elapsed 
 26.491   0.892  27.317