This page was generated on 2019-04-09 13:23:53 -0400 (Tue, 09 Apr 2019).
cellHTS2 2.47.1 Joseph Barry
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
URL: https://git.bioconductor.org/packages/cellHTS2 |
Branch: master |
Last Commit: 8a1a8cf |
Last Changed Date: 2019-01-04 13:24:45 -0400 (Fri, 04 Jan 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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> ## 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, 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/Rtmps7JjgW/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/Rtmps7JjgW/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/Rtmps7JjgW/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/Rtmps7JjgW/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/Rtmps7JjgW/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/Rtmps7JjgW/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/Rtmps7JjgW/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/Rtmps7JjgW/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
41.519 2.031 44.667