Pol Sola-Santos
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MAIT |
| Branch: RELEASE_3_9 |
| Last Commit: e7a92f9 |
| Last Changed Date: 2019-05-02 11:53:50 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:31:32 -0400 (Wed, 16 Oct 2019).
| Package 908/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MAIT 1.18.0 Pol Sola-Santos
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MAIT |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAIT.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MAIT_1.18.0.tar.gz |
| StartedAt: 2019-10-16 04:53:38 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:02:41 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 543.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAIT.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAIT.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MAIT_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MAIT.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MAIT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MAIT' version '1.18.0'
* 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 'MAIT' 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' call to 'rgl' in package code.
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
Biotransformations: no visible global function definition for 'data'
Biotransformations: no visible binding for global variable 'MAITtables'
Biotransformations: no visible global function definition for
'read.csv'
Biotransformations: no visible global function definition for
'read.csv2'
PLSDA: no visible global function definition for 'predict'
Validation: no visible global function definition for 'predict'
Validation: no visible global function definition for 'sd'
Validation: no visible global function definition for 'rainbow'
Validation: no visible global function definition for 'png'
Validation: no visible global function definition for 'boxplot'
Validation: no visible global function definition for 'legend'
Validation: no visible global function definition for 'title'
Validation: no visible global function definition for 'dev.off'
Validation: no visible binding for global variable 'sd'
computeSpectra: no visible global function definition for 'cor'
identifyMetabolites: no visible global function definition for 'data'
identifyMetabolites: no visible binding for global variable
'MAITtables'
identifyMetabolites: no visible global function definition for
'read.csv'
identifyMetabolites: no visible global function definition for
'write.table'
metaboliteTable: no visible global function definition for
'write.table'
peakAggregation: no visible global function definition for
'write.table'
peakAnnotation: no visible global function definition for 'data'
peakAnnotation: no visible binding for global variable 'MAITtables'
peakAnnotation: no visible global function definition for 'read.csv2'
plotBoxplot: no visible global function definition for 'png'
plotBoxplot: no visible global function definition for 'boxplot'
plotBoxplot: no visible global function definition for 'title'
plotBoxplot: no visible global function definition for 'dev.off'
plotHeatmap: no visible global function definition for 'p.adjust'
plotHeatmap : distCor: no visible global function definition for
'as.dist'
plotHeatmap : distCor: no visible global function definition for 'cor'
plotHeatmap : hclustWard: no visible global function definition for
'hclust'
plotHeatmap: no visible global function definition for
'colorRampPalette'
plotHeatmap: no visible global function definition for 'png'
plotHeatmap: no visible global function definition for 'legend'
plotHeatmap: no visible global function definition for 'dev.off'
plotPCA: no visible global function definition for 'prcomp'
plotPCA: no visible global function definition for 'png'
plotPCA: no visible global function definition for 'plot'
plotPCA: no visible global function definition for 'legend'
plotPCA: no visible global function definition for 'dev.off'
plotPLS: no visible global function definition for 'png'
plotPLS: no visible global function definition for 'plot'
plotPLS: no visible global function definition for 'legend'
plotPLS: no visible global function definition for 'dev.off'
sigPeaksTable: no visible global function definition for 'p.adjust'
sigPeaksTable: no visible global function definition for 'aggregate'
sigPeaksTable: no visible binding for global variable 'median'
sigPeaksTable: no visible global function definition for 'write.csv'
spectralAnova: no visible global function definition for 'lm'
spectralAnova: no visible global function definition for 'anova'
spectralAnova: no visible global function definition for 'p.adjust'
spectralFUN: no visible global function definition for 'p.adjust'
spectralKruskal: no visible global function definition for
'kruskal.test'
spectralKruskal: no visible global function definition for 'p.adjust'
spectralTStudent: no visible global function definition for 'lm'
spectralTStudent: no visible global function definition for 't.test'
spectralTStudent: no visible global function definition for 'p.adjust'
spectralWelch: no visible global function definition for 'lm'
spectralWelch: no visible global function definition for 't.test'
spectralWelch: no visible global function definition for 'p.adjust'
spectralWilcox: no visible global function definition for 'lm'
spectralWilcox: no visible global function definition for 'wilcox.test'
spectralWilcox: no visible global function definition for 'p.adjust'
writeExcelTable: no visible global function definition for 'write.csv'
writeParameterTable: no visible global function definition for
'write.csv'
Undefined global functions or variables:
MAITtables aggregate anova as.dist boxplot colorRampPalette cor data
dev.off hclust kruskal.test legend lm median p.adjust plot png prcomp
predict rainbow read.csv read.csv2 sd t.test title wilcox.test
write.csv write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "png",
"rainbow")
importFrom("graphics", "boxplot", "legend", "plot", "title")
importFrom("stats", "aggregate", "anova", "as.dist", "cor", "hclust",
"kruskal.test", "lm", "median", "p.adjust", "prcomp",
"predict", "sd", "t.test", "wilcox.test")
importFrom("utils", "data", "read.csv", "read.csv2", "write.csv",
"write.table")
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 or elapsed time > 5s
user system elapsed
parameters 17.27 0.05 17.31
Validation 16.65 0.24 17.24
classifRatioClasses 15.75 0.04 15.80
ovClassifRatio 13.05 0.12 13.17
ovClassifRatioTable 12.57 0.05 12.67
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Validation 17.92 0.11 18.03
classifRatioClasses 16.00 0.03 16.03
ovClassifRatioTable 14.13 0.00 14.12
ovClassifRatio 13.70 0.06 13.77
parameters 13.30 0.00 13.30
* 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-3.9-bioc/meat/MAIT.Rcheck/00check.log'
for details.
MAIT.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MAIT_1.18.0.tar.gz && rm -rf MAIT.buildbin-libdir && mkdir MAIT.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MAIT.buildbin-libdir MAIT_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MAIT_1.18.0.zip && rm MAIT_1.18.0.tar.gz MAIT_1.18.0.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 2189k 100 2189k 0 0 17.0M 0 --:--:-- --:--:-- --:--:-- 18.1M
install for i386
* installing *source* package 'MAIT' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'scores' in package 'MAIT'
Creating a new generic function for 'loadings' in package 'MAIT'
** help
*** installing help indices
converting help for package 'MAIT'
finding HTML links ... done
Biotransformations html
Database html
FisherLSD html
LSDResults html
MAIT-class html
finding level-2 HTML links ... done
MAIT.FeatureData-class html
MAIT.FeatureInfo-class html
MAIT.Parameters-class html
MAIT.PhenoData-class html
MAIT.RawData-class html
MAIT.Validation-class html
MAIT_dataSet html
MAITbuilder html
PCAplot3d html
PLSDA html
SearchCand html
Validation html
annotateBiotransf html
biotransformationsTable html
classNum html
classes html
classifRatioClasses html
featureID html
featureInfo html
featureSigID html
getScoresTable html
identifyMetabolites html
inBetween html
loadings html
metaboliteTable html
method html
model html
models html
negAdducts html
ovClassifRatio html
ovClassifRatioTable html
parameters html
pcaLoadings html
pcaModel html
pcaScores html
peakAggregation html
peakAnnotation html
plotBoxplot html
plotHeatmap html
plotPCA html
plotPLS html
plsLoadings html
plsModel html
plsScores html
posAdducts html
project html
pvalues html
pvaluesCorrection html
rawData html
removeOnePeakSpectra html
resultsPath html
retrieveSpectrum html
sampleProcessing html
scores html
selectK html
selectPLScomp html
sigPeaksTable html
spectralAnova html
spectralFUN html
spectralKruskal html
spectralSigFeatures html
spectralTStudent html
spectralWelch html
spectralWilcox html
successRatio html
writeExcelTable html
writeParameterTable 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 'MAIT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MAIT' as MAIT_1.18.0.zip
* DONE (MAIT)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MAIT' successfully unpacked and MD5 sums checked
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MAIT.Rcheck/examples_i386/MAIT-Ex.timings
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MAIT.Rcheck/examples_x64/MAIT-Ex.timings
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