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CHECK report for cellHTS2 on merida1

This page was generated on 2020-04-15 12:35:10 -0400 (Wed, 15 Apr 2020).

Package 242/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellHTS2 2.50.0
Joseph Barry
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/cellHTS2
Branch: RELEASE_3_10
Last Commit: 05030fc
Last Changed Date: 2019-10-29 13:07:50 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cellHTS2
Version: 2.50.0
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_2.50.0.tar.gz
StartedAt: 2020-04-15 01:00:39 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:05:13 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 273.9 seconds
RetCode: 0
Status:  OK 
CheckDir: cellHTS2.Rcheck
Warnings: 0

Command output

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###
### Running 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_2.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/cellHTS2.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.50.0’
* 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 ... NOTE
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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/cellHTS2.Rcheck/00check.log’
for details.



Installation output

cellHTS2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cellHTS2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)

Tests output

cellHTS2.Rcheck/tests/test.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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, 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 1.5-9.4 	 2020-03-24
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/RtmpPJmpOP/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/RtmpPJmpOP/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/RtmpPJmpOP/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/RtmpPJmpOP/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/RtmpPJmpOP/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/RtmpPJmpOP/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/RtmpPJmpOP/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/RtmpPJmpOP/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 
 41.702   2.098  44.758 

Example timings

cellHTS2.Rcheck/cellHTS2-Ex.timings

nameusersystemelapsed
Bscore2.5470.1232.696
ROC-class0.3010.0190.320
ROC0.9920.0271.037
annotate0.7420.0120.760
bdgpbiomart0.1930.0090.202
buildCellHTS20.2560.0020.258
cellHTS-class0.8070.0270.835
configurationAsScreenPlot1.5510.0451.598
configure0.6470.0050.652
convertOldCellHTS0.6380.0040.649
convertWellCoordinates0.0010.0000.000
data-KcViab0.1350.0060.143
data-KcViabSmall0.0100.0040.014
data-dualCh0.0100.0030.014
data-oldKcViabSmall0.0100.0040.013
getDynamicRange0.4740.0050.483
getEnVisionRawData0.0560.0010.061
getMeasureRepAgreement0.3550.0040.359
getTopTable1.0390.0071.048
getZfactor0.2770.0050.285
imageScreen0.9950.0091.011
normalizePlates1.2860.0101.304
oneRowPerId0.0030.0000.003
plotSpatialEffects1.6560.0191.681
readHTAnalystData0.7360.0030.747
readPlateList0.6380.0040.652
rsa0.7930.0070.803
scoreReplicates0.8930.0070.905
scores2calls0.9440.0080.956
setSettings0.0070.0030.010
spatialNormalization1.5020.0161.526
summarizeChannels1.7990.0121.817
summarizeReplicates1.0570.0091.076
templateDescriptionFile0.0020.0000.003
updateCellHTS0.0800.0060.085
write.tabdel0.0640.0040.069
writeReport0.0130.0050.017
writeTab0.0160.0040.023