Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:12 -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 CMA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CMA.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 343/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CMA 1.53.0 (landing page) Roman Hornung
| 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: CMA |
Version: 1.53.0 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CMA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CMA_1.53.0.tar.gz |
StartedAt: 2022-03-17 18:45:10 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 18:46:10 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 60.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CMA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CMA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CMA_1.53.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CMA.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 'CMA/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CMA' version '1.53.0' * 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 'CMA' 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 dependencies in R code ... NOTE 'library' or 'require' calls in package code: 'MASS' 'class' 'corpcor' 'e1071' 'gbm' 'glmnet' 'limma' 'mgcv' 'mvtnorm' 'nnet' 'plsgenomics' 'randomForest' 'st' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE ROCinternal: no visible binding for global variable 'xlab' ROCinternal: no visible binding for global variable 'ylab' ROCinternal: no visible binding for global variable 'main' ROCinternal: no visible binding for global variable 'lwd' ROCinternal: no visible global function definition for 'box' ROCinternal: no visible global function definition for 'text' characterplot: no visible global function definition for 'points' limmatest: no visible global function definition for 'lmFit' limmatest: no visible global function definition for 'contrasts.fit' limmatest: no visible global function definition for 'eBayes' limmatest: no visible global function definition for 'classifyTestsF' plotprob: no visible global function definition for 'axis' plotprob: no visible global function definition for 'points' plotprob: no visible global function definition for 'abline' plotprob: no visible global function definition for 'text' rfe: no visible binding for global variable 'cost' rfe: no visible binding for global variable 'svm' Planarplot,matrix-numeric-missing: no visible global function definition for 'points' boxplot,evaloutput: no visible binding for global variable 'main' compare,list: no visible global function definition for 'par' compare,list: no visible global function definition for 'dev.interactive' compare,list: no visible binding for global variable 'main' fdaCMA,matrix-numeric-missing: no visible global function definition for 'points' flexdaCMA,matrix-numeric-missing: no visible global function definition for 'gam' flexdaCMA,matrix-numeric-missing: no visible global function definition for 'points' gbmCMA,matrix-numeric-missing: no visible binding for global variable 'n.minobsinnode' gbmCMA,matrix-numeric-missing: no visible binding for global variable 'bag.fraction' gbmCMA,matrix-numeric-missing: no visible binding for global variable 'n.trees' gbmCMA,matrix-numeric-missing: no visible binding for global variable 'verbose' gbmCMA,matrix-numeric-missing: no visible binding for global variable 'gbm.fit' knnCMA,matrix-numeric-missing: no visible global function definition for 'knn' ldaCMA,matrix-numeric-missing: no visible global function definition for 'lda' nnetCMA,matrix-numeric-missing: no visible binding for global variable 'size' nnetCMA,matrix-numeric-missing: no visible binding for global variable 'MaxNWts' nnetCMA,matrix-numeric-missing: no visible global function definition for 'class.ind' plot,genesel-missing: no visible binding for global variable 'xlab' plot,genesel-missing: no visible binding for global variable 'ylab' plot,genesel-missing: no visible binding for global variable 'main' plot,genesel-missing: no visible binding for global variable 'cex.lab' plot,genesel-missing: no visible binding for global variable 'ylim' plot,genesel-missing: no visible binding for global variable 'barplot' plot,genesel-missing: no visible global function definition for 'par' plot,genesel-missing: no visible global function definition for 'dev.interactive' plot,tuningresult-missing: no visible binding for global variable 'main' plot,tuningresult-missing: no visible binding for global variable 'xlab' plot,tuningresult-missing: no visible binding for global variable 'ylab' plot,tuningresult-missing: no visible binding for global variable 'ylim' plot,tuningresult-missing: no visible binding for global variable 'lines' plot,tuningresult-missing: no visible global function definition for 'abline' plot,tuningresult-missing: no visible binding for global variable 'contour' plot,tuningresult-missing: no visible global function definition for 'points' pls_ldaCMA,matrix-numeric-missing: no visible global function definition for 'pls.regression' pls_ldaCMA,matrix-numeric-missing: no visible global function definition for 'transformy' pls_ldaCMA,matrix-numeric-missing: no visible global function definition for 'lda' pls_lrCMA,matrix-numeric-missing: no visible global function definition for 'pls.regression' pls_lrCMA,matrix-numeric-missing: no visible global function definition for 'transformy' pls_rfCMA,matrix-numeric-missing: no visible global function definition for 'pls.regression' pls_rfCMA,matrix-numeric-missing: no visible global function definition for 'transformy' pls_rfCMA,matrix-numeric-missing: no visible global function definition for 'randomForest' prediction,data.frame-missing-data.frame-formula: no visible global function definition for 'predicition' qdaCMA,matrix-numeric-missing: no visible global function definition for 'qda' rfCMA,matrix-numeric-missing: no visible global function definition for 'randomForest' shrinkldaCMA,matrix-numeric-missing: no visible global function definition for 'cov.shrink' svmCMA,matrix-numeric-missing: no visible binding for global variable 'cost' weighted.mcr,character-character-numeric-character-matrix-numeric: no visible global function definition for 'make.positive.definite' weighted.mcr,character-character-numeric-character-matrix-numeric: no visible global function definition for 'pmvnorm' weighted.mcr,character-character-numeric-character-matrix-numeric: no visible global function definition for 'rmvnorm' wmc,matrix-numeric-numeric: no visible global function definition for 'make.positive.definite' wmc,matrix-numeric-numeric: no visible global function definition for 'pmvnorm' wmc,matrix-numeric-numeric: no visible global function definition for 'rmvnorm' Undefined global functions or variables: MaxNWts abline axis bag.fraction barplot box cex.lab class.ind classifyTestsF contour contrasts.fit cost cov.shrink dev.interactive eBayes gam gbm.fit knn lda lines lmFit lwd main make.positive.definite n.minobsinnode n.trees par pls.regression pmvnorm points predicition qda randomForest rmvnorm size svm text transformy verbose xlab ylab ylim Consider adding importFrom("grDevices", "dev.interactive") importFrom("graphics", "abline", "axis", "barplot", "box", "contour", "lines", "par", "points", "text") 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 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 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: 2 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/CMA.Rcheck/00check.log' for details.
CMA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CMA ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'CMA' ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'CMA' finding HTML links ... done CMA-package html ElasticNetCMA-methods html ElasticNetCMA html GeneSelection-methods html GeneSelection html GenerateLearningsets html LassoCMA-methods html LassoCMA html Planarplot-methods html Planarplot html best html boxplot html classification-methods html classification html cloutput-class html clvarseloutput-class html compBoostCMA-methods html compBoostCMA html compare-methods html compare html dldaCMA-methods html dldaCMA html evaloutput-class html evaluation-methods html evaluation html fdaCMA-methods html fdaCMA html filter html flexdaCMA-methods html flexdaCMA html ftable html gbmCMA-methods html gbmCMA html genesel-class html golub html internals html join-methods html join html khan html knnCMA-methods html knnCMA html ldaCMA-methods html ldaCMA html learningsets-class html nnetCMA-methods html nnetCMA html obsinfo html pknnCMA-methods html pknnCMA html plot,cloutput-method html plot,genesel-method html plot,tuningresult-method html plrCMA-methods html plrCMA html pls_ldaCMA-methods html pls_ldaCMA html pls_lrCMA-methods html pls_lrCMA html pls_rfCMA-methods html pls_rfCMA html pnnCMA-methods html pnnCMA html prediction-methods html prediction html predoutput-class html qdaCMA-methods html qdaCMA html rfCMA-methods html rfCMA html roc html scdaCMA-methods html scdaCMA html shrinkldaCMA-methods html shrinkldaCMA html summary html svmCMA-methods html svmCMA html toplist html tune-methods html tune html tuningresult-class html varseloutput-class html weighted_mcr-methods html weighted_mcr html wmc-methods html wmc html wmcr_result-class 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 (CMA) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'RBGL' is missing or broken done
CMA.Rcheck/CMA-Ex.timings
name | user | system | elapsed | |
ElasticNetCMA | 0.89 | 0.10 | 0.98 | |
GeneSelection | 0.08 | 0.01 | 0.10 | |
GenerateLearningsets | 0 | 0 | 0 | |
LassoCMA | 0.18 | 0.05 | 0.24 | |
Planarplot | 0.19 | 0.00 | 0.19 | |
classification | 0 | 0 | 0 | |
compBoostCMA | 1.01 | 0.16 | 1.17 | |
compare | 0 | 0 | 0 | |
dldaCMA | 0.08 | 0.03 | 0.11 | |
evaluation | 0.08 | 0.00 | 0.08 | |
fdaCMA | 0.11 | 0.00 | 0.11 | |
flexdaCMA | 0.12 | 0.03 | 0.15 | |
gbmCMA | 1.17 | 0.05 | 1.22 | |
golub | 0.02 | 0.00 | 0.02 | |
khan | 0.03 | 0.00 | 0.03 | |
knnCMA | 0.08 | 0.04 | 0.13 | |
ldaCMA | 0 | 0 | 0 | |
nnetCMA | 0.06 | 0.00 | 0.06 | |
pknnCMA | 0.05 | 0.02 | 0.06 | |
plrCMA | 0.12 | 0.08 | 0.20 | |
pls_ldaCMA | 0 | 0 | 0 | |
pls_lrCMA | 0.89 | 0.12 | 1.02 | |
pls_rfCMA | 0.04 | 0.02 | 0.05 | |
pnnCMA | 0.04 | 0.00 | 0.04 | |
prediction | 0 | 0 | 0 | |
qdaCMA | 0.08 | 0.00 | 0.08 | |
rfCMA | 0.06 | 0.00 | 0.06 | |
scdaCMA | 0.05 | 0.01 | 0.07 | |
shrinkldaCMA | 0.06 | 0.00 | 0.06 | |
svmCMA | 0.20 | 0.03 | 0.24 | |
tune | 0 | 0 | 0 | |
weighted_mcr | 1.16 | 0.27 | 1.42 | |