Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:56:23 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE CRImage PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 390/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CRImage 1.36.0 Henrik Failmezger
| malbec2 | Linux (Ubuntu 18.04.4 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: CRImage |
Version: 1.36.0 |
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CRImage.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CRImage_1.36.0.tar.gz |
StartedAt: 2020-10-17 03:02:06 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 03:04:35 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 149.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CRImage.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CRImage.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CRImage_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CRImage.Rcheck' * using R version 4.0.3 (2020-10-10) * 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 '1.36.0' * 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 5.7Mb 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 * 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 '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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CRImage.Rcheck/00check.log' for details.
CRImage.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CRImage_1.36.0.tar.gz && rm -rf CRImage.buildbin-libdir && mkdir CRImage.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CRImage.buildbin-libdir CRImage_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CRImage_1.36.0.zip && rm CRImage_1.36.0.tar.gz CRImage_1.36.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 6442k 100 6442k 0 0 44.7M 0 --:--:-- --:--:-- --:--:-- 47.3M install for i386 * 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 install for x64 * installing *source* package 'CRImage' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'CRImage' as CRImage_1.36.0.zip * DONE (CRImage) * installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library' package 'CRImage' successfully unpacked and MD5 sums checked
CRImage.Rcheck/examples_i386/CRImage-Ex.timings
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CRImage.Rcheck/examples_x64/CRImage-Ex.timings
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