Joseph Barry
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/cellHTS2 |
| git_branch: RELEASE_3_18 |
| git_last_commit: 3fe8e7d |
| git_last_commit_date: 2023-10-24 09:38:36 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:35:50 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 295/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cellHTS2 2.66.0 (landing page) Joseph Barry
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the cellHTS2 package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: cellHTS2 |
| Version: 2.66.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:cellHTS2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings cellHTS2_2.66.0.tar.gz |
| StartedAt: 2024-04-15 21:00:00 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 21:08:24 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 503.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cellHTS2.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:cellHTS2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings cellHTS2_2.66.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/cellHTS2.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘cellHTS2/DESCRIPTION’ ... OK
* this is package ‘cellHTS2’ version ‘2.66.0’
* 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
19.905 0.753 20.577
* 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 1.5-9.9 2024-03-01
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 function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
Warning: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
Warning: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
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 outside the scale range
(`stat_bin()`).
Warning: Removed 446 rows containing non-finite outside the scale range
(`stat_binhex()`).
Warning: Computation failed in `stat_binhex()`.
Caused by error in `compute_group()`:
! The package "hexbin" is required for `stat_bin_hex()`.
Warning: Removed 24 rows containing non-finite outside the scale range
(`stat_qq()`).
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 24 rows containing non-finite outside the scale range
(`stat_bin()`).
Warning: Removed 502 rows containing non-finite outside the scale range
(`stat_binhex()`).
Warning: Computation failed in `stat_binhex()`.
Caused by error in `compute_group()`:
! The package "hexbin" is required for `stat_bin_hex()`.
Warning: Removed 24 rows containing non-finite outside the scale range
(`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 1.5-9.9 2024-03-01
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 function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
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 1.5-9.9 2024-03-01
Loading required package: grid
Warning: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
Warning: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
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 function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
Warning: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
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 1.5-9.9 2024-03-01
Loading required package: grid
Warning: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
Warning: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
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 function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
Warning: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
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-3.18-bioc/meat/cellHTS2.Rcheck/00check.log’
for details.
cellHTS2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL cellHTS2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-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)
cellHTS2.Rcheck/tests/test.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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 1.5-9.9 2024-03-01
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/RtmpmWGH4i/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/RtmpmWGH4i/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 function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
4: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
5: The plotPlateArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'.
6: The imageScreenArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'.
7: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
8: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
9: In sprintf("Left: raw, right: normalized", r) :
one argument not used by format 'Left: raw, right: normalized'
10: 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/RtmpmWGH4i/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'.
3: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
4: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
>
> ######
> ## 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/RtmpmWGH4i/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'.
3: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
4: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
>
> ######
> ## 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/RtmpmWGH4i/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'.
3: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
4: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
>
> ######
> ## 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/RtmpmWGH4i/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/RtmpmWGH4i/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 function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
4: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
5: The plotPlateArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'.
6: The imageScreenArgs argument is deprecated. Please use the settings infrastructure as explained in '?setSettings'.
7: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
8: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
9: 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/RtmpmWGH4i/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'.
3: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
4: The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
>
> proc.time()
user system elapsed
26.774 0.852 27.542
cellHTS2.Rcheck/cellHTS2-Ex.timings
| name | user | system | elapsed | |
| Bscore | 2.382 | 0.176 | 2.558 | |
| ROC-class | 0.190 | 0.000 | 0.191 | |
| ROC | 0.776 | 0.012 | 0.788 | |
| annotate | 0.620 | 0.024 | 0.645 | |
| bdgpbiomart | 0.185 | 0.000 | 0.185 | |
| buildCellHTS2 | 0.228 | 0.000 | 0.228 | |
| cellHTS-class | 0.577 | 0.024 | 0.602 | |
| configurationAsScreenPlot | 0.864 | 0.008 | 0.872 | |
| configure | 0.528 | 0.000 | 0.529 | |
| convertOldCellHTS | 0.485 | 0.004 | 0.489 | |
| convertWellCoordinates | 0 | 0 | 0 | |
| data-KcViab | 0.128 | 0.000 | 0.129 | |
| data-KcViabSmall | 0.009 | 0.000 | 0.010 | |
| data-dualCh | 0.011 | 0.000 | 0.010 | |
| data-oldKcViabSmall | 0.009 | 0.000 | 0.009 | |
| getDynamicRange | 0.42 | 0.00 | 0.42 | |
| getEnVisionRawData | 0.021 | 0.000 | 0.022 | |
| getMeasureRepAgreement | 0.325 | 0.008 | 0.334 | |
| getTopTable | 0.833 | 0.020 | 0.854 | |
| getZfactor | 0.221 | 0.000 | 0.221 | |
| imageScreen | 0.705 | 0.008 | 0.712 | |
| normalizePlates | 0.925 | 0.000 | 0.924 | |
| oneRowPerId | 0.000 | 0.003 | 0.003 | |
| plotSpatialEffects | 1.221 | 0.016 | 1.237 | |
| readHTAnalystData | 0.538 | 0.008 | 0.548 | |
| readPlateList | 0.396 | 0.000 | 0.396 | |
| rsa | 0.537 | 0.000 | 0.537 | |
| scoreReplicates | 0.734 | 0.004 | 0.738 | |
| scores2calls | 0.785 | 0.040 | 0.825 | |
| setSettings | 0.004 | 0.000 | 0.003 | |
| spatialNormalization | 1.223 | 0.000 | 1.223 | |
| summarizeChannels | 1.338 | 0.000 | 1.338 | |
| summarizeReplicates | 0.685 | 0.012 | 0.696 | |
| templateDescriptionFile | 0.001 | 0.000 | 0.001 | |
| updateCellHTS | 0.062 | 0.000 | 0.063 | |
| write.tabdel | 0.048 | 0.000 | 0.048 | |
| writeReport | 0.009 | 0.000 | 0.009 | |
| writeTab | 0.015 | 0.000 | 0.015 | |