Roman Hornung
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/CMA |
| git_branch: RELEASE_3_13 |
| git_last_commit: 2f87021 |
| git_last_commit_date: 2021-05-19 11:41:03 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:00 -0400 (Fri, 15 Oct 2021).
|
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 337/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CMA 1.50.0 (landing page) Roman Hornung
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: CMA |
| Version: 1.50.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CMA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CMA_1.50.0.tar.gz |
| StartedAt: 2021-10-14 21:16:19 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:18:02 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 103.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CMA.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CMA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CMA_1.50.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CMA.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.50.0'
* 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
* 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 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 ...
** 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/CMA.Rcheck/00check.log'
for details.
CMA.Rcheck/00install.out
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###
### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CMA_1.50.0.tar.gz && rm -rf CMA.buildbin-libdir && mkdir CMA.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CMA.buildbin-libdir CMA_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CMA_1.50.0.zip && rm CMA_1.50.0.tar.gz CMA_1.50.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 817k 100 817k 0 0 2071k 0 --:--:-- --:--:-- --:--:-- 2074k
install for i386
* 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
install for x64
* installing *source* package 'CMA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CMA' as CMA_1.50.0.zip
* DONE (CMA)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CMA' successfully unpacked and MD5 sums checked
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CMA.Rcheck/examples_i386/CMA-Ex.timings
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CMA.Rcheck/examples_x64/CMA-Ex.timings
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