Pol Sola-Santos
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/MAIT |
| Branch: RELEASE_3_10 |
| Last Commit: 59e57b2 |
| Last Changed Date: 2019-10-29 13:09:05 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:09:19 -0400 (Wed, 15 Apr 2020).
| Package 945/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MAIT 1.20.0 Pol Sola-Santos
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MAIT |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MAIT_1.20.0.tar.gz |
| StartedAt: 2020-04-15 02:35:55 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:42:00 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 364.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAIT.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MAIT_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/MAIT.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAIT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAIT’ version ‘1.20.0’
* 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 ‘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
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
classifRatioClasses 22.484 0.064 22.595
Validation 18.340 0.068 18.448
ovClassifRatio 18.256 0.076 18.359
parameters 17.544 0.056 17.661
ovClassifRatioTable 16.280 0.044 16.351
* 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-3.10-bioc/meat/MAIT.Rcheck/00check.log’
for details.
MAIT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MAIT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘MAIT’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning message: replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’ Creating a new generic function for ‘scores’ in package ‘MAIT’ Creating a new generic function for ‘loadings’ in package ‘MAIT’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’ ** testing if installed package keeps a record of temporary installation path * DONE (MAIT)
MAIT.Rcheck/MAIT-Ex.timings
| name | user | system | elapsed | |
| Biotransformations | 2.048 | 0.016 | 2.081 | |
| LSDResults | 0.848 | 0.000 | 0.849 | |
| MAITbuilder | 0.020 | 0.000 | 0.016 | |
| Validation | 18.340 | 0.068 | 18.448 | |
| classNum | 0.004 | 0.000 | 0.004 | |
| classes | 0.000 | 0.000 | 0.004 | |
| classifRatioClasses | 22.484 | 0.064 | 22.595 | |
| featureID | 0.760 | 0.000 | 0.759 | |
| featureInfo | 1.064 | 0.004 | 1.067 | |
| featureSigID | 1.012 | 0.004 | 1.016 | |
| getScoresTable | 1.084 | 0.008 | 1.092 | |
| identifyMetabolites | 2.072 | 0.020 | 2.097 | |
| loadings | 2.780 | 0.000 | 2.844 | |
| metaboliteTable | 1.324 | 0.008 | 1.335 | |
| method | 0.000 | 0.000 | 0.003 | |
| model | 2.904 | 0.012 | 2.925 | |
| models | 0.904 | 0.000 | 0.906 | |
| ovClassifRatio | 18.256 | 0.076 | 18.359 | |
| ovClassifRatioTable | 16.280 | 0.044 | 16.351 | |
| parameters | 17.544 | 0.056 | 17.661 | |
| pcaLoadings | 1.084 | 0.000 | 1.086 | |
| pcaModel | 1.104 | 0.004 | 1.119 | |
| pcaScores | 0.968 | 0.004 | 0.972 | |
| peakAggregation | 0.016 | 0.000 | 0.015 | |
| peakAnnotation | 0 | 0 | 0 | |
| plotBoxplot | 1.312 | 0.000 | 1.314 | |
| plotHeatmap | 3.456 | 0.032 | 3.491 | |
| plotPCA | 0.812 | 0.008 | 0.821 | |
| plotPLS | 2.568 | 0.004 | 2.577 | |
| plsLoadings | 2.732 | 0.004 | 2.738 | |
| plsModel | 2.784 | 0.000 | 2.787 | |
| plsScores | 2.556 | 0.000 | 2.560 | |
| pvalues | 0.840 | 0.000 | 0.837 | |
| pvaluesCorrection | 0.804 | 0.000 | 0.806 | |
| rawData | 0.004 | 0.000 | 0.004 | |
| resultsPath | 0.944 | 0.000 | 0.946 | |
| sampleProcessing | 0 | 0 | 0 | |
| scores | 2.980 | 0.024 | 3.016 | |
| sigPeaksTable | 1.288 | 0.000 | 1.288 | |
| spectralSigFeatures | 1.224 | 0.000 | 1.229 | |