Pol Sola-Santos
| Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/MAIT |
| git_branch: devel |
| git_last_commit: 2f8e62b |
| git_last_commit_date: 2024-10-29 09:55:51 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:46 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| 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 | ||||
| Package 1139/2277 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MAIT 1.41.0 (landing page) Pol Sola-Santos
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the MAIT package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: MAIT |
| Version: 1.41.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MAIT_1.41.0.tar.gz |
| StartedAt: 2025-01-11 08:07:14 -0000 (Sat, 11 Jan 2025) |
| EndedAt: 2025-01-11 08:16:56 -0000 (Sat, 11 Jan 2025) |
| EllapsedTime: 581.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAIT.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MAIT_1.41.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MAIT.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAIT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAIT’ version ‘1.41.0’
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) classes.Rd:5: Lost braces
5 | Function \code{classes} extracts the class names of a link{MAIT-class} object as a vector.
| ^
checkRd: (-1) parameters.Rd:5: Lost braces
5 | Function \code{parameters} extracts the slot link{MAIT.Parameters-class} of a \code{\link{MAIT-class}} object. This class contains all the parameters that have been used in the previous functions. Typing a summary of this object, a matrix version of the parameters is obtained.
| ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
MAIT-class.Rd: xsAnnotate
MAIT.FeatureData-class.Rd: xsAnnotate
MAIT.FeatureInfo-class.Rd: xsAnnotate
MAIT.PhenoData-class.Rd: xsAnnotate
MAIT.RawData-class.Rd: xsAnnotate
MAIT.Validation-class.Rd: xsAnnotate
peakAnnotation.Rd: xsAnnotate, groupCorr, xsAnnotate-class
rawData.Rd: xsAnnotate, xsAnnotate-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 19.064 0.447 19.562
parameters 17.934 0.172 18.151
ovClassifRatioTable 17.784 0.175 18.004
ovClassifRatio 17.804 0.104 17.956
classifRatioClasses 17.761 0.123 17.937
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/MAIT.Rcheck/00check.log’
for details.
MAIT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MAIT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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 ** 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)
MAIT.Rcheck/MAIT-Ex.timings
| name | user | system | elapsed | |
| Biotransformations | 1.073 | 0.044 | 1.123 | |
| LSDResults | 0.931 | 0.112 | 1.046 | |
| MAITbuilder | 0.022 | 0.004 | 0.027 | |
| Validation | 19.064 | 0.447 | 19.562 | |
| classNum | 0.004 | 0.000 | 0.004 | |
| classes | 0.004 | 0.000 | 0.004 | |
| classifRatioClasses | 17.761 | 0.123 | 17.937 | |
| featureID | 0.958 | 0.028 | 0.988 | |
| featureInfo | 0.999 | 0.032 | 1.034 | |
| featureSigID | 0.969 | 0.008 | 0.980 | |
| getScoresTable | 1.011 | 0.016 | 1.030 | |
| identifyMetabolites | 1.687 | 0.036 | 1.726 | |
| loadings | 1.836 | 0.056 | 1.896 | |
| metaboliteTable | 1.722 | 0.004 | 1.730 | |
| method | 0.004 | 0.000 | 0.003 | |
| model | 1.735 | 0.008 | 1.748 | |
| models | 0.955 | 0.000 | 0.957 | |
| ovClassifRatio | 17.804 | 0.104 | 17.956 | |
| ovClassifRatioTable | 17.784 | 0.175 | 18.004 | |
| parameters | 17.934 | 0.172 | 18.151 | |
| pcaLoadings | 1.017 | 0.000 | 1.019 | |
| pcaModel | 1.136 | 0.008 | 1.147 | |
| pcaScores | 1.019 | 0.000 | 1.022 | |
| peakAggregation | 0.009 | 0.000 | 0.008 | |
| peakAnnotation | 0.000 | 0.000 | 0.001 | |
| plotBoxplot | 1.129 | 0.020 | 1.152 | |
| plotHeatmap | 2.835 | 0.015 | 2.858 | |
| plotPCA | 1.039 | 0.000 | 1.041 | |
| plotPLS | 1.677 | 0.000 | 1.682 | |
| plsLoadings | 1.645 | 0.000 | 1.649 | |
| plsModel | 1.639 | 0.012 | 1.656 | |
| plsScores | 1.613 | 0.020 | 1.637 | |
| pvalues | 0.939 | 0.000 | 0.941 | |
| pvaluesCorrection | 0.910 | 0.000 | 0.912 | |
| rawData | 0.003 | 0.000 | 0.004 | |
| resultsPath | 0.916 | 0.000 | 0.919 | |
| sampleProcessing | 0 | 0 | 0 | |
| scores | 1.676 | 0.006 | 1.686 | |
| sigPeaksTable | 1.052 | 0.000 | 1.054 | |
| spectralSigFeatures | 0.934 | 0.000 | 0.936 | |