Back to Multiple platform build/check report for BioC 3.20:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 383/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CMA 1.64.0  (landing page)
Roman Hornung
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/CMA
git_branch: RELEASE_3_20
git_last_commit: e471c68
git_last_commit_date: 2024-10-29 09:29:21 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for CMA on teran2

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.

raw results


Summary

Package: CMA
Version: 1.64.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CMA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CMA_1.64.0.tar.gz
StartedAt: 2024-11-20 00:32:56 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 00:34:07 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 71.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CMA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CMA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CMA_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/CMA.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CMA’ version ‘1.64.0’
* 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
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/CMA.Rcheck/00check.log’
for details.


Installation output

CMA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL CMA
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘CMA’ ...
** 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)

Tests output


Example timings

CMA.Rcheck/CMA-Ex.timings

nameusersystemelapsed
ElasticNetCMA0.8940.1512.056
GeneSelection0.0630.0090.072
GenerateLearningsets0.0050.0000.006
LassoCMA0.1190.0070.126
Planarplot0.1130.0060.119
classification000
compBoostCMA0.6300.0110.656
compare0.0000.0000.001
dldaCMA0.0800.0060.086
evaluation0.0600.0020.062
fdaCMA0.0570.0030.059
flexdaCMA0.0930.0030.142
gbmCMA1.3540.0121.591
golub0.0180.0010.019
khan0.0280.0010.029
knnCMA0.2750.0070.305
ldaCMA000
nnetCMA0.0340.0030.037
pknnCMA0.0410.0040.045
plrCMA0.1330.0050.138
pls_ldaCMA000
pls_lrCMA0.4800.0100.572
pls_rfCMA0.0290.0020.031
pnnCMA0.0250.0020.027
prediction000
qdaCMA0.0590.0060.073
rfCMA0.0390.0000.039
scdaCMA0.0530.0070.060
shrinkldaCMA0.0520.0050.057
svmCMA0.2230.0040.255
tune000
weighted_mcr1.2710.0471.435