Pol Sola-Santos
| Snapshot Date: 2019-02-12 17:02:41 -0500 (Tue, 12 Feb 2019) |
| URL: https://git.bioconductor.org/packages/MAIT |
| Branch: RELEASE_3_8 |
| Last Commit: 5d28eeb |
| Last Changed Date: 2019-01-04 13:37:18 -0500 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-02-13 11:16:04 -0500 (Wed, 13 Feb 2019).
| Package 869/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MAIT 1.16.1 Pol Sola-Santos
| malbec1 | Linux (Ubuntu 16.04.1 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: 1.16.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MAIT_1.16.1.tar.gz |
| StartedAt: 2019-02-13 01:40:09 -0500 (Wed, 13 Feb 2019) |
| EndedAt: 2019-02-13 01:46:21 -0500 (Wed, 13 Feb 2019) |
| EllapsedTime: 371.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAIT.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MAIT_1.16.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/MAIT.Rcheck’
* using R version 3.5.2 (2018-12-20)
* 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 ‘1.16.1’
* 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
Validation 18.968 0.072 19.943
ovClassifRatioTable 18.316 0.048 19.295
ovClassifRatio 18.084 0.072 19.555
parameters 17.960 0.088 19.098
classifRatioClasses 17.808 0.092 19.258
* 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-3.8-bioc/meat/MAIT.Rcheck/00check.log’
for details.
MAIT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL MAIT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘MAIT’ ... ** 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 ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (MAIT)
MAIT.Rcheck/MAIT-Ex.timings
| name | user | system | elapsed | |
| Biotransformations | 1.344 | 0.020 | 1.464 | |
| LSDResults | 0.996 | 0.000 | 1.005 | |
| MAITbuilder | 0.024 | 0.000 | 0.024 | |
| Validation | 18.968 | 0.072 | 19.943 | |
| classNum | 0.004 | 0.000 | 0.005 | |
| classes | 0.004 | 0.004 | 0.006 | |
| classifRatioClasses | 17.808 | 0.092 | 19.258 | |
| featureID | 1.240 | 0.000 | 1.256 | |
| featureInfo | 1.160 | 0.000 | 1.458 | |
| featureSigID | 1.136 | 0.000 | 1.160 | |
| getScoresTable | 1.180 | 0.012 | 1.204 | |
| identifyMetabolites | 2.224 | 0.020 | 2.260 | |
| loadings | 2.924 | 0.016 | 3.056 | |
| metaboliteTable | 1.804 | 0.004 | 1.870 | |
| method | 0.000 | 0.004 | 0.004 | |
| model | 3.012 | 0.000 | 3.156 | |
| models | 1.052 | 0.000 | 1.354 | |
| ovClassifRatio | 18.084 | 0.072 | 19.555 | |
| ovClassifRatioTable | 18.316 | 0.048 | 19.295 | |
| parameters | 17.960 | 0.088 | 19.098 | |
| pcaLoadings | 1.048 | 0.004 | 1.108 | |
| pcaModel | 0.952 | 0.000 | 0.966 | |
| pcaScores | 1.236 | 0.004 | 1.335 | |
| peakAggregation | 0.012 | 0.000 | 0.014 | |
| peakAnnotation | 0 | 0 | 0 | |
| plotBoxplot | 1.288 | 0.004 | 1.366 | |
| plotHeatmap | 3.768 | 0.012 | 4.039 | |
| plotPCA | 1.048 | 0.004 | 1.063 | |
| plotPLS | 2.816 | 0.000 | 2.969 | |
| plsLoadings | 2.796 | 0.004 | 2.977 | |
| plsModel | 2.768 | 0.008 | 3.089 | |
| plsScores | 3.004 | 0.000 | 3.068 | |
| pvalues | 1.160 | 0.000 | 1.163 | |
| pvaluesCorrection | 1.156 | 0.000 | 1.155 | |
| rawData | 0.000 | 0.004 | 0.005 | |
| resultsPath | 1.144 | 0.000 | 1.146 | |
| sampleProcessing | 0 | 0 | 0 | |
| scores | 3.024 | 0.016 | 3.441 | |
| sigPeaksTable | 1.900 | 0.008 | 1.950 | |
| spectralSigFeatures | 1.172 | 0.000 | 1.229 | |