Joseph Barry
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/cellHTS2 |
| git_branch: RELEASE_3_13 |
| git_last_commit: 72c1d14 |
| git_last_commit_date: 2021-05-19 11:39:18 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:59 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the cellHTS2 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellHTS2.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 260/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cellHTS2 2.56.0 (landing page) Joseph Barry
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: cellHTS2 |
| Version: 2.56.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellHTS2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings cellHTS2_2.56.0.tar.gz |
| StartedAt: 2021-10-14 20:45:31 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 20:53:40 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 488.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cellHTS2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellHTS2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings cellHTS2_2.56.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/cellHTS2.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cellHTS2/DESCRIPTION' ... OK
* this is package 'cellHTS2' version '2.56.0'
* 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 whether package 'cellHTS2' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
KcViab 2.0Mb
R 1.1Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test.R'
OK
** running tests for arch 'x64' ...
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: 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/cellHTS2.Rcheck/00check.log'
for details.
cellHTS2.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/cellHTS2_2.56.0.tar.gz && rm -rf cellHTS2.buildbin-libdir && mkdir cellHTS2.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cellHTS2.buildbin-libdir cellHTS2_2.56.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL cellHTS2_2.56.0.zip && rm cellHTS2_2.56.0.tar.gz cellHTS2_2.56.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
79 1650k 79 1314k 0 0 2563k 0 --:--:-- --:--:-- --:--:-- 2561k
100 1650k 100 1650k 0 0 2811k 0 --:--:-- --:--:-- --:--:-- 2812k
install for i386
* installing *source* package 'cellHTS2' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cellHTS2'
finding HTML links ... done
Bscore html
Data html
ROC-class html
ROC html
annotate html
batch html
bdgpbiomart html
buildCellHTS2 html
cellHTS-class html
cellHTS2 html
configurationAsScreenPlot html
configure html
convertOldCellHTS html
convertWellCoordinates html
data-KcViab html
data-KcViabSmall html
data-dualCh html
data-oldKcViabSmall html
getDynamicRange html
getEnVisionRawData html
getMeasureRepAgreement html
getTopTable html
getZfactor html
gseaModule html
imageScreen html
intensityFiles html
normalizePlates html
oneRowPerId html
plate html
plateEffects html
plotSpatialEffects html
readHTAnalystData html
readPlateList html
rsa html
scoreReplicates html
scores2calls html
setSettings html
spatialNormalization html
state html
summarizeChannels html
summarizeReplicates html
templateDescriptionFile html
updateCellHTS html
wellAnno html
write.tabdel html
writeReport html
writeTab html
** 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
install for x64
* installing *source* package 'cellHTS2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellHTS2' as cellHTS2_2.56.0.zip
* DONE (cellHTS2)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'cellHTS2' successfully unpacked and MD5 sums checked
|
cellHTS2.Rcheck/tests_i386/test.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpYP8RC9/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpYP8RC9/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpYP8RC9/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpYP8RC9/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpYP8RC9/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpYP8RC9/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpYP8RC9/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpYP8RC9/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
27.68 3.09 31.09
|
cellHTS2.Rcheck/tests_x64/test.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpcTuEVn/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpcTuEVn/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpcTuEVn/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpcTuEVn/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpcTuEVn/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpcTuEVn/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpcTuEVn/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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpcTuEVn/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
29.85 2.53 32.51
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cellHTS2.Rcheck/examples_i386/cellHTS2-Ex.timings
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cellHTS2.Rcheck/examples_x64/cellHTS2-Ex.timings
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