Package: cellHTS2

Version: 2.44.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cellHTS2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cellHTS2_2.44.0.tar.gz

StartedAt: 2018-10-16 20:19:03 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:23:14 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 250.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cellHTS2.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cellHTS2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cellHTS2_2.44.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/cellHTS2.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellHTS2/DESCRIPTION’ ... OK
* this is package ‘cellHTS2’ version ‘2.44.0’
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Unknown package ‘cellHTS’ 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 sizes of PDF files under ‘inst/doc’ ... 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/cellHTS2.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cellHTS2
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘cellHTS2’ ...
** 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
* DONE (cellHTS2)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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 1.5-9.1 	 2013-03-22
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/Rtmp2Yr9ii/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/Rtmp2Yr9ii/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'. 
> 
> ######
> ## 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/Rtmp2Yr9ii/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/Rtmp2Yr9ii/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/Rtmp2Yr9ii/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/Rtmp2Yr9ii/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/Rtmp2Yr9ii/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'. 
> 
> ######
> ## 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/Rtmp2Yr9ii/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 
 40.695   2.028  44.828 

name	user	system	elapsed
Bscore	2.042	0.045	2.086
ROC-class	0.192	0.009	0.202
ROC	0.763	0.004	0.767
annotate	0.617	0.004	0.625
bdgpbiomart	0.176	0.007	0.183
buildCellHTS2	0.247	0.002	0.249
cellHTS-class	0.965	0.019	0.984
configurationAsScreenPlot	0.991	0.035	1.025
configure	0.580	0.006	0.587
convertOldCellHTS	0.479	0.003	0.484
convertWellCoordinates	0.001	0.000	0.002
data-KcViab	0.126	0.005	0.132
data-KcViabSmall	0.011	0.004	0.015
data-dualCh	0.012	0.004	0.016
data-oldKcViabSmall	0.010	0.004	0.014
getDynamicRange	0.421	0.005	0.426
getEnVisionRawData	0.049	0.002	0.050
getMeasureRepAgreement	0.429	0.005	0.435
getTopTable	0.988	0.010	0.999
getZfactor	0.250	0.002	0.252
imageScreen	0.754	0.004	0.759
normalizePlates	1.013	0.005	1.017
oneRowPerId	0.004	0.000	0.004
plotSpatialEffects	1.499	0.010	1.517
readHTAnalystData	0.677	0.003	0.686
readPlateList	0.526	0.004	0.532
rsa	0.722	0.003	0.730
scoreReplicates	0.858	0.004	0.873
scores2calls	0.874	0.004	0.889
setSettings	0.010	0.003	0.014
spatialNormalization	1.428	0.012	1.447
summarizeChannels	1.567	0.016	1.589
summarizeReplicates	0.746	0.007	0.755
templateDescriptionFile	0.002	0.001	0.003
updateCellHTS	0.098	0.003	0.102
write.tabdel	0.056	0.003	0.060
writeReport	0.012	0.002	0.014
writeTab	0.015	0.002	0.018