Dario Strbenac
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/ClassifyR |
| Branch: RELEASE_3_11 |
| Last Commit: 68d04d2 |
| Last Changed Date: 2020-04-27 14:42:08 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:17 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE ClassifyR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 304/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ClassifyR 2.8.0 Dario Strbenac
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: ClassifyR |
| Version: 2.8.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClassifyR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ClassifyR_2.8.0.tar.gz |
| StartedAt: 2020-10-17 02:38:05 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:55:59 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1074.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ClassifyR.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClassifyR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ClassifyR_2.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ClassifyR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ClassifyR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ClassifyR' version '2.8.0'
* 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 'ClassifyR' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpktZfwe/R.INSTALL2128198f63ab/ClassifyR/man/differentMeansSelection.Rd:40: file link 'rowttests' in package 'genefilter' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpktZfwe/R.INSTALL2128198f63ab/ClassifyR/man/distribution.Rd:32: file link 'stat_density' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpktZfwe/R.INSTALL2128198f63ab/ClassifyR/man/edgeRselection.Rd:45: file link 'edgeR' in package 'edgeR' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ClassifyR.Rcheck/00install.out' for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.posterior_probs : <anonymous>: no visible global function definition
for 'dmvnorm'
easyHardClassifierPredict,EasyHardClassifier-MultiAssayExperiment: no
visible binding for global variable 'measurements'
kTSPclassifier,DataFrame : <anonymous>: no visible global function
definition for 'Pairs'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable 'measurement'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable '..density..'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable 'legends grouping'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable 'key'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable 'value'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable 'ID'
rankingPlot,list : <anonymous> : <anonymous>: no visible global
function definition for 'first'
rankingPlot,list : <anonymous> : <anonymous>: no visible global
function definition for 'second'
rankingPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for 'first'
rankingPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for 'second'
runTest,DataFrame: no visible binding for global variable 'setsNodes'
runTestEasyHard,MultiAssayExperiment: no visible binding for global
variable 'setsNodes'
runTests,DataFrame: no visible binding for global variable 'setsNodes'
runTestsEasyHard,MultiAssayExperiment: no visible binding for global
variable 'setsNodes'
runTestsEasyHard,MultiAssayExperiment: no visible binding for global
variable '.iteration'
samplesMetricMap,list: no visible binding for global variable 'Class'
samplesMetricMap,list: no visible binding for global variable 'Group'
samplesMetricMap,list: no visible binding for global variable
'measurements'
samplesMetricMap,list: no visible binding for global variable 'name'
samplesMetricMap,list: no visible binding for global variable 'type'
samplesMetricMap,list: no visible binding for global variable 'Metric'
samplesMetricMap,matrix: no visible binding for global variable 'Class'
samplesMetricMap,matrix: no visible binding for global variable 'Group'
samplesMetricMap,matrix: no visible binding for global variable
'measurements'
samplesMetricMap,matrix: no visible binding for global variable 'name'
samplesMetricMap,matrix: no visible binding for global variable 'type'
samplesMetricMap,matrix: no visible binding for global variable
'Metric'
selectionPlot,list : <anonymous> : <anonymous>: no visible global
function definition for 'first'
selectionPlot,list : <anonymous> : <anonymous>: no visible global
function definition for 'second'
selectionPlot,list : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for 'first'
selectionPlot,list : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for 'second'
selectionPlot,list: no visible binding for global variable 'Freq'
Undefined global functions or variables:
..density.. .iteration Class Freq Group ID Metric Pairs dmvnorm first
key legends grouping measurement measurements name second setsNodes
type value
Consider adding
importFrom("base", "grouping")
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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ClassifyResult-class 10.61 1.19 65.81
DMDselection 5.77 0.53 6.30
runTests 4.07 0.36 63.55
distribution 2.48 0.47 44.29
selectionPlot 2.78 0.00 12.06
rankingPlot 2.64 0.00 14.80
previousTrained 2.18 0.04 41.03
previousSelection 1.65 0.05 40.65
elasticNetFeatures 1.27 0.03 42.02
elasticNetGLMinterface 1.14 0.00 39.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ClassifyResult-class 9.64 0.61 66.83
likelihoodRatioSelection 6.46 0.00 6.46
DMDselection 6.16 0.03 6.19
runTests 3.01 0.50 65.56
distribution 2.53 0.33 44.27
selectionPlot 2.81 0.00 12.46
rankingPlot 2.19 0.03 15.39
previousSelection 1.98 0.02 38.09
previousTrained 1.80 0.02 44.63
elasticNetFeatures 1.20 0.06 44.64
elasticNetGLMinterface 0.98 0.02 38.13
* 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: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/ClassifyR.Rcheck/00check.log'
for details.
ClassifyR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ClassifyR_2.8.0.tar.gz && rm -rf ClassifyR.buildbin-libdir && mkdir ClassifyR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ClassifyR.buildbin-libdir ClassifyR_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ClassifyR_2.8.0.zip && rm ClassifyR_2.8.0.tar.gz ClassifyR_2.8.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1004k 100 1004k 0 0 3960k 0 --:--:-- --:--:-- --:--:-- 4066k
install for i386
* installing *source* package 'ClassifyR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ClassifyR'
finding HTML links ... done
ClassifyResult-class html
finding level-2 HTML links ... done
DLDAinterface html
DMDselection html
EasyHardClassifier-class html
FeatureSetCollection-class html
FeatureSetCollectionOrNULL-class html
KolmogorovSmirnovSelection html
KullbackLeiblerSelection html
MixModelsListsSet-class html
NSCpredictInterface html
NSCselectionInterface html
NSCtrainInterface html
PredictParams-class html
ROCplot html
ResubstituteParams-class html
SVMinterface html
SelectParams-class html
SelectResult-class html
TrainParams-class html
TransformParams-class html
asthmaDataset html
bartlettSelection html
calcPerformance html
characterOrDataFrame-class html
classifyInterface html
differentMeansSelection html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpktZfwe/R.INSTALL2128198f63ab/ClassifyR/man/differentMeansSelection.Rd:40: file link 'rowttests' in package 'genefilter' does not exist and so has been treated as a topic
distribution html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpktZfwe/R.INSTALL2128198f63ab/ClassifyR/man/distribution.Rd:32: file link 'stat_density' in package 'ggplot2' does not exist and so has been treated as a topic
dlda-class html
easyHardClassifier html
easyHardFeatures html
edgeRselection html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpktZfwe/R.INSTALL2128198f63ab/ClassifyR/man/edgeRselection.Rd:45: file link 'edgeR' in package 'edgeR' does not exist and so has been treated as a topic
edgesToHubNetworks html
elasticNetFeatures html
elasticNetGLMinterface html
featureSetSummary html
fisherDiscriminant html
forestFeatures html
functionOrList-class html
functionOrNULL-class html
getLocationsAndScales html
integerOrNumeric-class html
interactorDifferences html
kTSPclassifier html
knnInterface html
leveneSelection html
likelihoodRatioSelection html
limmaSelection html
listOrCharacterOrNULL-class html
listOrNULL-class html
mixmodels html
multnet-class html
naiveBayesKernel html
networkCorrelationsSelection html
pairsDifferencesSelection html
pamrtrained-class html
performancePlot html
plotFeatureClasses html
previousSelection html
previousTrained html
randomForest-class html
randomForestInterface html
rankingPlot html
runTest html
runTests html
samplesMetricMap html
selectionPlot html
subtractFromLocation html
svm-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 'ClassifyR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ClassifyR' as ClassifyR_2.8.0.zip
* DONE (ClassifyR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ClassifyR' successfully unpacked and MD5 sums checked
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ClassifyR.Rcheck/examples_i386/ClassifyR-Ex.timings
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ClassifyR.Rcheck/examples_x64/ClassifyR-Ex.timings
|