Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:54 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the TCGAbiolinks package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TCGAbiolinks.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 1899/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TCGAbiolinks 2.20.1 (landing page) Tiago Chedraoui Silva
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: TCGAbiolinks |
Version: 2.20.1 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TCGAbiolinks_2.20.1.tar.gz |
StartedAt: 2021-10-14 11:50:18 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:58:28 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 489.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TCGAbiolinks.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TCGAbiolinks_2.20.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/TCGAbiolinks.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TCGAbiolinks’ version ‘2.20.1’ * 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 ‘TCGAbiolinks’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: R 1.6Mb data 3.7Mb * 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 ... WARNING '::' or ':::' import not declared from: ‘sesameData’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GDCquery : <anonymous>: no visible binding for global variable ‘submitter_id’ GDCquery : <anonymous>: no visible binding for global variable ‘is_ffpe’ TCGAanalyze_DEA: no visible binding for global variable ‘barcode’ TCGAanalyze_DEA: no visible binding for global variable ‘clinical’ TCGAquery_recount2: no visible binding for global variable ‘rse_gene’ TCGAtumor_purity: no visible binding for global variable ‘Tumor.purity’ TCGAvisualize_oncoprint: no visible binding for global variable ‘value’ TCGAvisualize_starburst: no visible global function definition for ‘values’ readExonQuantification: no visible binding for global variable ‘exon’ readExonQuantification: no visible binding for global variable ‘coordinates’ readGeneExpressionQuantification : <anonymous>: no visible binding for '<<-' assignment to ‘assay.list’ readGeneExpressionQuantification: no visible binding for global variable ‘assay.list’ Undefined global functions or variables: Tumor.purity assay.list barcode clinical coordinates exon is_ffpe rse_gene submitter_id value values * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TCGAanalyze_LevelTab 15.315 0.043 15.359 GDCquery_clinic 13.345 0.683 31.403 TCGAanalyze_DEA 13.059 0.179 13.237 TCGAanalyze_Filtering 11.187 0.104 11.292 TCGAvisualize_PCA 6.675 0.064 6.740 TCGAanalyze_Stemness 6.656 0.068 6.724 TCGAanalyze_Normalization 6.321 0.168 6.489 GDCdownload 2.452 0.323 38.457 GDCprepare_clinic 1.929 0.172 47.475 matchedMetExp 0.592 0.011 5.007 GDCquery 0.586 0.008 5.525 getResults 0.542 0.010 5.458 getManifest 0.494 0.009 6.670 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/TCGAbiolinks.Rcheck/00check.log’ for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘TCGAbiolinks’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** 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 (TCGAbiolinks)
TCGAbiolinks.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(TCGAbiolinks) > > test_check("TCGAbiolinks") | | 0% |========================== | 50% ~0 s remaining |====================================================|100% ~0 s remaining |====================================================|100% Completed after 0 s | | 0% |========================== | 50% ~0 s remaining |====================================================|100% ~0 s remaining |====================================================|100% Completed after 0 s [1] "I need about 1 minute to finish complete Enrichment analysis GO[BP,MF,CC] and Pathways... " [1] "GO Enrichment Analysis BP completed....done" [1] "GO Enrichment Analysis MF completed....done" [1] "GO Enrichment Analysis CC completed....done" [1] "Pathway Enrichment Analysis completed....done" ══ Skipped tests ═══════════════════════════════════════════════════════════════ • On Bioconductor (21) [ FAIL 0 | WARN 4 | SKIP 21 | PASS 45 ] > > proc.time() user system elapsed 50.246 3.117 64.802
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
name | user | system | elapsed | |
GDCdownload | 2.452 | 0.323 | 38.457 | |
GDCprepare | 0.001 | 0.000 | 0.000 | |
GDCprepare_clinic | 1.929 | 0.172 | 47.475 | |
GDCquery | 0.586 | 0.008 | 5.525 | |
GDCquery_ATAC_seq | 0.525 | 0.027 | 1.025 | |
GDCquery_Maf | 0.001 | 0.000 | 0.000 | |
GDCquery_clinic | 13.345 | 0.683 | 31.403 | |
PanCancerAtlas_subtypes | 0.014 | 0.000 | 0.015 | |
TCGAVisualize_volcano | 0.259 | 0.000 | 0.259 | |
TCGA_MolecularSubtype | 0.175 | 0.000 | 0.175 | |
TCGAanalyze_DEA | 13.059 | 0.179 | 13.237 | |
TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
TCGAanalyze_DMC | 0.907 | 0.086 | 0.993 | |
TCGAanalyze_EA | 0.000 | 0.001 | 0.000 | |
TCGAanalyze_EAcomplete | 3.363 | 0.079 | 3.442 | |
TCGAanalyze_Filtering | 11.187 | 0.104 | 11.292 | |
TCGAanalyze_LevelTab | 15.315 | 0.043 | 15.359 | |
TCGAanalyze_Normalization | 6.321 | 0.168 | 6.489 | |
TCGAanalyze_Pathview | 0.000 | 0.000 | 0.001 | |
TCGAanalyze_Stemness | 6.656 | 0.068 | 6.724 | |
TCGAanalyze_SurvivalKM | 0.091 | 0.000 | 0.091 | |
TCGAanalyze_survival | 2.400 | 0.052 | 2.452 | |
TCGAprepare_Affy | 0.000 | 0.000 | 0.001 | |
TCGAquery_MatchedCoupledSampleTypes | 0.002 | 0.000 | 0.002 | |
TCGAquery_SampleTypes | 0.001 | 0.000 | 0.001 | |
TCGAquery_recount2 | 0.000 | 0.000 | 0.001 | |
TCGAquery_subtype | 0.007 | 0.000 | 0.007 | |
TCGAtumor_purity | 0.057 | 0.000 | 0.057 | |
TCGAvisualize_EAbarplot | 2.171 | 0.020 | 2.191 | |
TCGAvisualize_Heatmap | 1.771 | 0.024 | 1.795 | |
TCGAvisualize_PCA | 6.675 | 0.064 | 6.740 | |
TCGAvisualize_meanMethylation | 2.206 | 0.020 | 2.225 | |
TCGAvisualize_oncoprint | 0.000 | 0.000 | 0.001 | |
TCGAvisualize_starburst | 0.001 | 0.000 | 0.001 | |
UseRaw_afterFilter | 0 | 0 | 0 | |
colDataPrepare | 0.134 | 0.004 | 0.607 | |
dmc.non.parametric | 0.132 | 0.032 | 0.163 | |
dmc.non.parametric.se | 0.215 | 0.012 | 0.228 | |
gaiaCNVplot | 0.018 | 0.008 | 0.027 | |
getAdjacencyBiogrid | 0.002 | 0.000 | 0.002 | |
getDataCategorySummary | 1.183 | 0.027 | 4.744 | |
getGDCInfo | 0.021 | 0.000 | 0.154 | |
getGDCprojects | 0.032 | 0.004 | 0.144 | |
getLinkedOmicsData | 0.001 | 0.000 | 0.000 | |
getMC3MAF | 0.001 | 0.000 | 0.000 | |
getManifest | 0.494 | 0.009 | 6.670 | |
getNbCases | 0 | 0 | 0 | |
getNbFiles | 0.000 | 0.001 | 0.000 | |
getProjectSummary | 0.000 | 0.000 | 0.001 | |
getResults | 0.542 | 0.010 | 5.458 | |
getSampleFilesSummary | 0.351 | 0.003 | 1.492 | |
getTSS | 0.001 | 0.000 | 0.001 | |
gliomaClassifier | 0.000 | 0.000 | 0.001 | |
isServeOK | 0.020 | 0.000 | 0.148 | |
matchedMetExp | 0.592 | 0.011 | 5.007 | |