Henrik Failmezger
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/CRImage |
| git_branch: master |
| git_last_commit: d67c92b |
| git_last_commit_date: 2021-10-26 11:57:17 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:16 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the CRImage package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CRImage.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 418/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CRImage 1.43.0 (landing page) Henrik Failmezger
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CRImage |
| Version: 1.43.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CRImage.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CRImage_1.43.0.tar.gz |
| StartedAt: 2022-03-17 18:49:46 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:51:05 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 79.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CRImage.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CRImage.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CRImage_1.43.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CRImage.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CRImage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CRImage' version '1.43.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'CRImage' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
extdata 5.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
'DNAcopy' 'aCGH'
Please remove these calls from your code.
':::' call which should be '::': 'aCGH:::combine.func'
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
Phansalkar_threshold: no visible global function definition for 'sd'
SauvolaThreshold: no visible global function definition for 'sd'
calculateMeanStdTarget: no visible global function definition for 'sd'
calculateOtsu: no visible global function definition for 'optimize'
classificationAperio: no visible global function definition for
'write.table'
classificationAperio: no visible global function definition for
'read.table'
classifyCells: no visible global function definition for 'predict'
classifyPen: no visible global function definition for 'predict'
colorCorrection: no visible global function definition for 'sd'
correctCopyNumber : Myansari.test.default: no visible global function
definition for 'complete.cases'
correctCopyNumber : Myansari.test.default: no visible global function
definition for 'pnorm'
correctCopyNumber : Myansari.test.default : ccia: no visible global
function definition for 'qnorm'
correctCopyNumber : Myansari.test.default : ccia: no visible global
function definition for 'uniroot'
correctCopyNumber : Myansari.test.default: no visible global function
definition for 'uniroot'
correctCopyNumber: no visible global function definition for 'quantile'
correctCopyNumber: no visible global function definition for 'median'
determineCellularity: no visible global function definition for
'colorRampPalette'
determineCellularity: no visible global function definition for
'col2rgb'
findSlices: no visible global function definition for 'cutree'
findSlices: no visible global function definition for 'hclust'
findSlices: no visible global function definition for 'dist'
findSlices: no visible global function definition for 'col2rgb'
kernelSmoother: no visible global function definition for 'dist'
labelCells: no visible global function definition for 'points'
labelCells: no visible global function definition for 'title'
labelCells : refresh: no visible global function definition for
'points'
labelCells : refresh: no visible global function definition for 'title'
labelCells : refresh: no visible global function definition for
'write.table'
labelCells : keydown: no visible global function definition for
'write.table'
labelCells : keydown: no visible global function definition for 'title'
labelCells : dragmousedown: no visible global function definition for
'grconvertX'
labelCells : dragmousedown: no visible global function definition for
'grconvertY'
labelCells : dragmousemove: no visible global function definition for
'grconvertX'
labelCells : dragmousemove: no visible global function definition for
'grconvertY'
labelCells : dragmousemove: no visible global function definition for
'lines'
labelCells : dragmouseup: no visible global function definition for
'chull'
labelCells : dragmouseup: no visible global function definition for
'grconvertX'
labelCells : dragmouseup: no visible global function definition for
'grconvertY'
labelCells: no visible global function definition for
'setGraphicsEventHandlers'
labelCells: no visible global function definition for
'getGraphicsEvent'
numberOfNeighbors: no visible global function definition for 'dist'
plotCorrectedCN: no visible global function definition for 'par'
plotCorrectedCN: no visible global function definition for 'segments'
plotCorrectedCN: no visible global function definition for 'title'
plotImage: no visible global function definition for 'grey'
plotImage: no visible global function definition for 'rgb'
processAperio: no visible global function definition for 'write.table'
processAperio: no visible global function definition for 'col2rgb'
segmentStructures: no visible global function definition for 'predict'
Undefined global functions or variables:
chull col2rgb colorRampPalette complete.cases cutree dist
getGraphicsEvent grconvertX grconvertY grey hclust lines median
optimize par pnorm points predict qnorm quantile read.table rgb sd
segments setGraphicsEventHandlers title uniroot write.table
Consider adding
importFrom("grDevices", "chull", "col2rgb", "colorRampPalette",
"getGraphicsEvent", "grey", "rgb",
"setGraphicsEventHandlers")
importFrom("graphics", "grconvertX", "grconvertY", "lines", "par",
"points", "segments", "title")
importFrom("stats", "complete.cases", "cutree", "dist", "hclust",
"median", "optimize", "pnorm", "predict", "qnorm",
"quantile", "sd", "uniroot")
importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/CRImage.Rcheck/00check.log'
for details.
CRImage.Rcheck/00install.out
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CRImage
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CRImage' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CRImage'
finding HTML links ... done
CRImage-internal html
CRImage-package html
SauvolaThreshold html
calculateCellularity html
calculateMeanStdTarget html
calculateOtsu html
classifyCells html
colorCorrection html
convertHSVToRGB html
convertLABToRGB html
convertRGBToHSV html
convertRGBToLAB html
correctCopyNumber html
createBinaryImage html
createClassifier html
labelCells html
plotCorrectedCN html
processAperio html
segmentImage 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
* DONE (CRImage)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'makecdfenv' is missing or broken
done
CRImage.Rcheck/CRImage-Ex.timings
| name | user | system | elapsed | |
| CRImage-package | 0.25 | 0.01 | 0.26 | |
| SauvolaThreshold | 0.20 | 0.00 | 0.21 | |
| calculateCellularity | 2.13 | 0.88 | 3.00 | |
| calculateMeanStdTarget | 0.67 | 0.42 | 1.09 | |
| calculateOtsu | 0.19 | 0.03 | 0.22 | |
| classifyCells | 1.69 | 0.47 | 2.16 | |
| colorCorrection | 0.68 | 0.33 | 1.02 | |
| convertHSVToRGB | 0.24 | 0.15 | 0.39 | |
| convertLABToRGB | 0.25 | 0.10 | 0.34 | |
| convertRGBToHSV | 1.80 | 0.14 | 1.94 | |
| convertRGBToLAB | 0.31 | 0.20 | 0.51 | |
| correctCopyNumber | 0.08 | 0.00 | 0.08 | |
| createBinaryImage | 0.39 | 0.44 | 0.83 | |
| createClassifier | 0.15 | 0.00 | 0.16 | |
| labelCells | 0 | 0 | 0 | |
| plotCorrectedCN | 0.11 | 0.00 | 0.10 | |
| processAperio | 0.02 | 0.00 | 0.02 | |
| segmentImage | 0 | 0 | 0 | |