Pol Sola-Santos
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/MAIT |
| git_branch: master |
| git_last_commit: 3a65444 |
| git_last_commit_date: 2021-10-26 12:16:52 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:55 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the MAIT package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAIT.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1043/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MAIT 1.29.0 (landing page) Pol Sola-Santos
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MAIT |
| Version: 1.29.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAIT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MAIT_1.29.0.tar.gz |
| StartedAt: 2022-03-17 19:28:30 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:33:56 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 325.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAIT.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAIT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MAIT_1.29.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MAIT.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.29.0'
* 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
* 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 '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 '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 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", "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 (user + system) or elapsed time > 5s
user system elapsed
Validation 11.20 0.06 11.27
parameters 10.73 0.05 10.78
ovClassifRatioTable 10.13 0.01 10.15
classifRatioClasses 9.89 0.09 9.98
ovClassifRatio 9.07 0.03 9.10
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/MAIT.Rcheck/00check.log'
for details.
MAIT.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MAIT
###
##############################################################################
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (MAIT)
Making 'packages.html' ... done
MAIT.Rcheck/MAIT-Ex.timings
| name | user | system | elapsed | |
| Biotransformations | 0.64 | 0.11 | 0.75 | |
| LSDResults | 0.51 | 0.01 | 0.53 | |
| MAITbuilder | 0.02 | 0.00 | 0.01 | |
| Validation | 11.20 | 0.06 | 11.27 | |
| classNum | 0.00 | 0.02 | 0.01 | |
| classes | 0.02 | 0.00 | 0.02 | |
| classifRatioClasses | 9.89 | 0.09 | 9.98 | |
| featureID | 0.78 | 0.02 | 0.80 | |
| featureInfo | 0.78 | 0.00 | 0.78 | |
| featureSigID | 0.78 | 0.00 | 0.78 | |
| getScoresTable | 0.73 | 0.03 | 0.77 | |
| identifyMetabolites | 1.19 | 0.01 | 1.20 | |
| loadings | 1.84 | 0.05 | 1.89 | |
| metaboliteTable | 0.88 | 0.03 | 0.91 | |
| method | 0.01 | 0.00 | 0.01 | |
| model | 1.66 | 0.05 | 1.70 | |
| models | 0.52 | 0.02 | 0.54 | |
| ovClassifRatio | 9.07 | 0.03 | 9.10 | |
| ovClassifRatioTable | 10.13 | 0.01 | 10.15 | |
| parameters | 10.73 | 0.05 | 10.78 | |
| pcaLoadings | 0.52 | 0.01 | 0.53 | |
| pcaModel | 0.53 | 0.00 | 0.53 | |
| pcaScores | 0.53 | 0.02 | 0.55 | |
| peakAggregation | 0.00 | 0.02 | 0.01 | |
| peakAnnotation | 0 | 0 | 0 | |
| plotBoxplot | 0.72 | 0.03 | 0.77 | |
| plotHeatmap | 2.09 | 0.06 | 2.15 | |
| plotPCA | 0.57 | 0.02 | 0.58 | |
| plotPLS | 1.87 | 0.01 | 1.89 | |
| plsLoadings | 2.05 | 0.02 | 2.07 | |
| plsModel | 1.58 | 0.01 | 1.59 | |
| plsScores | 1.68 | 0.02 | 1.72 | |
| pvalues | 0.58 | 0.03 | 0.61 | |
| pvaluesCorrection | 0.80 | 0.01 | 0.81 | |
| rawData | 0.00 | 0.02 | 0.02 | |
| resultsPath | 0.73 | 0.00 | 0.73 | |
| sampleProcessing | 0 | 0 | 0 | |
| scores | 2.22 | 0.03 | 2.25 | |
| sigPeaksTable | 0.67 | 0.02 | 0.69 | |
| spectralSigFeatures | 0.80 | 0.01 | 0.81 | |