CMA 1.28.1
Christoph Bernau
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CMA | | Last Changed Rev: 116541 / Revision: 116712 | | Last Changed Date: 2016-04-19 03:14:28 -0700 (Tue, 19 Apr 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CMA_1.28.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/CMA.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CMA’ version ‘1.28.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CMA’ can be installed ... [3s/3s] 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 loading without being on the library search path ... 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’
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’
rfe: no visible binding for global variable ‘cost’
rfe: no visible binding for global variable ‘svm’
boxplot,evaloutput: no visible binding for global variable ‘main’
compare,list: no visible binding for global variable ‘main’
flexdaCMA,matrix-numeric-missing: no visible global function definition
for ‘gam’
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 : .local: no visible binding for global variable
‘xlab’
plot,genesel-missing : .local: no visible binding for global variable
‘ylab’
plot,genesel-missing : .local: no visible binding for global variable
‘main’
plot,genesel-missing : .local: no visible binding for global variable
‘cex.lab’
plot,genesel-missing : .local: no visible binding for global variable
‘ylim’
plot,tuningresult-missing : .local: no visible binding for global
variable ‘main’
plot,tuningresult-missing : .local: no visible binding for global
variable ‘xlab’
plot,tuningresult-missing : .local: no visible binding for global
variable ‘ylab’
plot,tuningresult-missing : .local: no visible binding for global
variable ‘ylim’
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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] 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
‘/home/biocbuild/bbs-3.2-bioc/meat/CMA.Rcheck/00check.log’
for details.