Roman Hornung
| Snapshot Date: 2026-01-01 13:45 -0500 (Thu, 01 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/CMA |
| git_branch: RELEASE_3_22 |
| git_last_commit: 70c568b |
| git_last_commit_date: 2025-10-29 10:00:45 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-05 11:57 -0500 (Mon, 05 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 | ||||
| Package 398/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CMA 1.68.0 (landing page) Roman Hornung
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the CMA package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: CMA |
| Version: 1.68.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CMA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CMA_1.68.0.tar.gz |
| StartedAt: 2026-01-01 22:07:26 -0500 (Thu, 01 Jan 2026) |
| EndedAt: 2026-01-01 22:08:29 -0500 (Thu, 01 Jan 2026) |
| EllapsedTime: 63.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CMA.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CMA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CMA_1.68.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CMA.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘CMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CMA’ version ‘1.68.0’
* 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 for sufficient/correct file permissions ... 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 code 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’
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 ... NOTE
checkRd: (-1) learningsets-class.Rd:28: Lost braces in \itemize; meant \describe ?
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/CMA.Rcheck/00check.log’
for details.
CMA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CMA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘CMA’ ... ** this is package ‘CMA’ version ‘1.68.0’ ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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)
CMA.Rcheck/CMA-Ex.timings
| name | user | system | elapsed | |
| ElasticNetCMA | 1.189 | 0.125 | 1.314 | |
| GeneSelection | 0.094 | 0.009 | 0.102 | |
| GenerateLearningsets | 0.009 | 0.000 | 0.008 | |
| LassoCMA | 0.180 | 0.008 | 0.188 | |
| Planarplot | 0.206 | 0.007 | 0.213 | |
| classification | 0.001 | 0.000 | 0.000 | |
| compBoostCMA | 0.931 | 0.008 | 0.939 | |
| compare | 0 | 0 | 0 | |
| dldaCMA | 0.114 | 0.008 | 0.122 | |
| evaluation | 0.086 | 0.002 | 0.088 | |
| fdaCMA | 0.083 | 0.002 | 0.086 | |
| flexdaCMA | 0.139 | 0.003 | 0.142 | |
| gbmCMA | 1.470 | 0.010 | 1.482 | |
| golub | 0.026 | 0.001 | 0.027 | |
| khan | 0.040 | 0.000 | 0.041 | |
| knnCMA | 0.112 | 0.003 | 0.115 | |
| ldaCMA | 0.001 | 0.000 | 0.000 | |
| nnetCMA | 0.05 | 0.00 | 0.05 | |
| pknnCMA | 0.060 | 0.002 | 0.062 | |
| plrCMA | 0.202 | 0.008 | 0.211 | |
| pls_ldaCMA | 0 | 0 | 0 | |
| pls_lrCMA | 0.672 | 0.009 | 0.682 | |
| pls_rfCMA | 0.043 | 0.000 | 0.042 | |
| pnnCMA | 0.036 | 0.002 | 0.039 | |
| prediction | 0 | 0 | 0 | |
| qdaCMA | 0.091 | 0.002 | 0.092 | |
| rfCMA | 0.060 | 0.001 | 0.060 | |
| scdaCMA | 0.077 | 0.004 | 0.080 | |
| shrinkldaCMA | 0.069 | 0.001 | 0.070 | |
| svmCMA | 0.312 | 0.003 | 0.315 | |
| tune | 0 | 0 | 0 | |
| weighted_mcr | 1.395 | 0.063 | 1.457 | |