Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:12 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1072/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MAIT 1.33.0 (landing page) Pol Sola-Santos
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: MAIT |
Version: 1.33.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MAIT_1.33.0.tar.gz |
StartedAt: 2023-02-07 06:37:33 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 06:46:19 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 525.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: MAIT.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MAIT_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MAIT.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘MAIT/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MAIT’ version ‘1.33.0’ * 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 ‘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 classifRatioClasses 18.954 0.128 19.088 Validation 18.626 0.116 18.875 ovClassifRatioTable 17.946 0.096 18.043 ovClassifRatio 17.905 0.076 17.983 parameters 17.837 0.078 17.916 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘MAIT_Vignette.Rnw’... failed ERROR Errors in running code in vignettes: when running code in ‘MAIT_Vignette.Rnw’ ... + mustWork = TRUE) > MAIT <- sampleProcessing(dataDir = cdfFiles, project = "MAIT_Demo", + snThres = 2, rtStep = 0.03) Warning in parallel::mccollect(wait = FALSE, timeout = 1) : 1 parallel job did not deliver a result When sourcing ‘MAIT_Vignette.R’: Error: wrong args for environment subassignment Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘MAIT_Vignette.Rnw’ using Sweave Loading required package: CAMERA Loading required package: Biobase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: ProtGenerics Attaching package: ‘ProtGenerics’ The following object is masked from ‘package:stats’: smooth This is MSnbase version 2.25.1 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: ‘MSnbase’ The following object is masked from ‘package:base’: trimws This is xcms version 3.21.0 Attaching package: ‘xcms’ The following object is masked from ‘package:stats’: sigma Loading required package: pls Attaching package: ‘pls’ The following object is masked from ‘package:stats’: loadings Attaching package: ‘MAIT’ The following objects are masked from ‘package:pls’: loadings, scores The following object is masked from ‘package:mzR’: model The following object is masked from ‘package:BiocGenerics’: plotPCA The following object is masked from ‘package:stats’: loadings Warning in parallel::mccollect(wait = FALSE, timeout = 1) : 1 parallel job did not deliver a result Error: processing vignette 'MAIT_Vignette.Rnw' failed with diagnostics: chunk 2 (label = sampleProcessing) Error in reducer$value.cache[[as.character(idx)]] <- values : wrong args for environment subassignment --- failed re-building ‘MAIT_Vignette.Rnw’ SUMMARY: processing the following file failed: ‘MAIT_Vignette.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/MAIT.Rcheck/00check.log’ for details.
MAIT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MAIT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 ** 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 | 1.083 | 0.020 | 1.105 | |
LSDResults | 0.914 | 0.008 | 0.922 | |
MAITbuilder | 0.022 | 0.004 | 0.026 | |
Validation | 18.626 | 0.116 | 18.875 | |
classNum | 0.005 | 0.000 | 0.015 | |
classes | 0.005 | 0.000 | 0.004 | |
classifRatioClasses | 18.954 | 0.128 | 19.088 | |
featureID | 0.937 | 0.000 | 0.936 | |
featureInfo | 0.874 | 0.000 | 0.874 | |
featureSigID | 0.886 | 0.000 | 0.886 | |
getScoresTable | 0.913 | 0.020 | 0.933 | |
identifyMetabolites | 1.595 | 0.028 | 1.624 | |
loadings | 1.720 | 0.012 | 1.734 | |
metaboliteTable | 1.646 | 0.014 | 1.660 | |
method | 0.004 | 0.000 | 0.003 | |
model | 1.668 | 0.008 | 1.677 | |
models | 0.906 | 0.000 | 0.907 | |
ovClassifRatio | 17.905 | 0.076 | 17.983 | |
ovClassifRatioTable | 17.946 | 0.096 | 18.043 | |
parameters | 17.837 | 0.078 | 17.916 | |
pcaLoadings | 0.954 | 0.006 | 0.959 | |
pcaModel | 0.963 | 0.000 | 0.963 | |
pcaScores | 0.961 | 0.008 | 0.970 | |
peakAggregation | 0.009 | 0.000 | 0.009 | |
peakAnnotation | 0 | 0 | 0 | |
plotBoxplot | 1.116 | 0.004 | 1.120 | |
plotHeatmap | 2.931 | 0.036 | 2.899 | |
plotPCA | 0.953 | 0.000 | 0.953 | |
plotPLS | 1.663 | 0.000 | 1.663 | |
plsLoadings | 1.649 | 0.004 | 1.653 | |
plsModel | 1.591 | 0.003 | 1.593 | |
plsScores | 1.590 | 0.004 | 1.595 | |
pvalues | 0.894 | 0.002 | 0.896 | |
pvaluesCorrection | 0.901 | 0.000 | 0.901 | |
rawData | 0.004 | 0.000 | 0.004 | |
resultsPath | 0.876 | 0.000 | 0.876 | |
sampleProcessing | 0 | 0 | 0 | |
scores | 1.653 | 0.020 | 1.673 | |
sigPeaksTable | 1.032 | 0.008 | 1.040 | |
spectralSigFeatures | 0.923 | 0.000 | 0.923 | |