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This page was generated on 2024-03-04 11:38:58 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 295/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellHTS2 2.67.1  (landing page)
Joseph Barry
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/cellHTS2
git_branch: devel
git_last_commit: e6c1ecb
git_last_commit_date: 2024-02-14 11:49:19 -0500 (Wed, 14 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for cellHTS2 on merida1


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.

raw results


Summary

Package: cellHTS2
Version: 2.67.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellHTS2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellHTS2_2.67.1.tar.gz
StartedAt: 2024-03-02 01:24:01 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 01:33:29 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 567.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: cellHTS2.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellHTS2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellHTS2_2.67.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/cellHTS2.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellHTS2/DESCRIPTION’ ... OK
* this is package ‘cellHTS2’ version ‘2.67.1’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'cellHTS2' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/cellHTS2.Rcheck/00install.out’ for details.
* 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 whether 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
Bscore 5.186    0.1   6.124
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/cellHTS2.Rcheck/00check.log’
for details.



Installation output

cellHTS2.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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
Warning: Package 'cellHTS2' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning: Package 'cellHTS2' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (cellHTS2)

Tests output

cellHTS2.Rcheck/tests/test.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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, 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 message:
Package 'cellHTS2' is deprecated and will be removed from Bioconductor
  version 3.20 
> 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)2024-03-02 01:32:17.720 R[77345:936125828] XType: com.apple.fonts is not accessible.
2024-03-02 01:32:17.720 R[77345:936125828] XType: XTFontStaticRegistry is enabled.

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/Rtmp1HzxXM/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/Rtmp1HzxXM/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/Rtmp1HzxXM/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/Rtmp1HzxXM/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/Rtmp1HzxXM/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/Rtmp1HzxXM/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/Rtmp1HzxXM/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/Rtmp1HzxXM/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 
 58.608   3.202  71.369 

Example timings

cellHTS2.Rcheck/cellHTS2-Ex.timings

nameusersystemelapsed
Bscore5.1860.1006.124
ROC-class0.5150.0550.655
ROC1.9560.0262.298
annotate1.5600.0231.843
bdgpbiomart0.3170.0130.388
buildCellHTS20.5860.0080.696
cellHTS-class1.9850.0872.420
configurationAsScreenPlot2.5400.2153.238
configure1.3800.0311.620
convertOldCellHTS1.0890.0131.259
convertWellCoordinates0.0000.0010.001
data-KcViab0.2240.0070.264
data-KcViabSmall0.0160.0040.023
data-dualCh0.0180.0040.026
data-oldKcViabSmall0.0150.0030.022
getDynamicRange0.9730.0161.125
getEnVisionRawData0.0510.0050.084
getMeasureRepAgreement0.8230.0160.967
getTopTable2.1740.0262.479
getZfactor0.5530.0070.629
imageScreen1.7800.0262.013
normalizePlates2.3320.0302.653
oneRowPerId0.0050.0000.007
plotSpatialEffects3.3630.0433.965
readHTAnalystData1.3540.0181.613
readPlateList0.9740.0191.228
rsa1.4070.0211.608
scoreReplicates1.5370.0221.795
scores2calls1.8660.0282.237
setSettings0.0070.0150.026
spatialNormalization2.7460.0353.172
summarizeChannels3.1260.0353.691
summarizeReplicates1.5800.0181.867
templateDescriptionFile0.0010.0020.005
updateCellHTS0.1840.0070.216
write.tabdel0.1140.0050.136
writeReport0.0160.0040.023
writeTab0.0230.0040.030