Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-30 11:35:58 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
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 2138/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TCGAbiolinks 2.32.0 (landing page) Tiago Chedraoui Silva
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the TCGAbiolinks package: - 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 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. |
Package: TCGAbiolinks |
Version: 2.32.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TCGAbiolinks_2.32.0.tar.gz |
StartedAt: 2024-05-30 00:13:03 -0400 (Thu, 30 May 2024) |
EndedAt: 2024-05-30 00:22:31 -0400 (Thu, 30 May 2024) |
EllapsedTime: 568.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TCGAbiolinks.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TCGAbiolinks_2.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/TCGAbiolinks.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TCGAbiolinks’ version ‘2.32.0’ * package encoding: UTF-8 * 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 6.4Mb sub-directories of 1Mb or more: R 1.6Mb data 4.5Mb * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘dnet’ * checking S3 generic/method consistency ... WARNING print: function(x, ...) print.header: function(text, type) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GDCprepare_clinic: no visible binding for global variable ‘bcr_patient_barcode’ GDCprepare_clinic: no visible binding for global variable ‘days_to_last_followup’ GDCprepare_clinic: no visible binding for global variable ‘vital_status’ GDCquery : <anonymous>: no visible binding for global variable ‘submitter_id’ GDCquery : <anonymous>: no visible binding for global variable ‘is_ffpe’ GDCquery_clinic : <anonymous>: no visible binding for global variable ‘submitter_id’ GDCquery_clinic : <anonymous>: no visible global function definition for ‘across’ GDCquery_clinic : <anonymous>: no visible global function definition for ‘everything’ 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 binding for global variable ‘gene_name’ TCGAvisualize_starburst: no visible binding for global variable ‘geFDR2’ TCGAvisualize_starburst: no visible binding for global variable ‘logFC’ TCGAvisualize_starburst: no visible binding for global variable ‘meFDR2’ TCGAvisualize_starburst: no visible binding for global variable ‘threshold.starburst’ TCGAvisualize_starburst: no visible binding for global variable ‘starburst.status’ colDataPrepare: no visible binding for global variable ‘sample_submitter_id’ colDataPrepare: no visible binding for global variable ‘submitter_id’ readExonQuantification: no visible binding for global variable ‘exon’ readExonQuantification: no visible binding for global variable ‘coordinates’ readSingleCellAnalysis : <anonymous>: no visible global function definition for ‘Read10X’ read_gene_expression_quantification : <anonymous>: no visible binding for '<<-' assignment to ‘assay.list’ read_gene_expression_quantification: no visible binding for global variable ‘assay.list’ Undefined global functions or variables: Read10X Tumor.purity across assay.list barcode bcr_patient_barcode clinical coordinates days_to_last_followup everything exon geFDR2 gene_name is_ffpe logFC meFDR2 rse_gene sample_submitter_id starburst.status submitter_id threshold.starburst value vital_status * 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_DEA 11.402 0.703 12.205 getManifest 10.524 0.258 100.948 TCGAanalyze_LevelTab 5.824 0.200 6.083 GDCquery 1.711 0.054 10.325 GDCprepare_clinic 1.205 0.139 32.131 matchedMetExp 1.040 0.051 10.093 getResults 0.770 0.028 7.158 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 2 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/TCGAbiolinks.Rcheck/00check.log’ for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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" [ FAIL 0 | WARN 0 | SKIP 24 | PASS 32 ] ══ Skipped tests (24) ══════════════════════════════════════════════════════════ • On Bioconductor (24): 'test-prepare-download.R:4:5', 'test-prepare-download.R:49:5', 'test-prepare-download.R:92:5', 'test-prepare-download.R:102:5', 'test-prepare-download.R:124:5', 'test-prepare-download.R:145:5', 'test-prepare-download.R:164:5', 'test-prepare-download.R:183:5', 'test-prepare-download.R:199:5', 'test-prepare-download.R:209:5', 'test-prepare-download.R:221:5', 'test-prepare-download.R:246:5', 'test-prepare-download.R:286:5', 'test-prepare-download.R:316:5', 'test-prepare-download.R:347:5', 'test-prepare-download.R:381:5', 'test-query-clinical.R:13:5', 'test-query-clinical.R:69:5', 'test-query.R:5:5', 'test-query.R:15:5', 'test-query.R:44:5', 'test-query.R:86:5', 'test-query.R:127:5', 'test-query.R:147:5' [ FAIL 0 | WARN 0 | SKIP 24 | PASS 32 ] > > proc.time() user system elapsed 48.145 2.438 51.062
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
name | user | system | elapsed | |
GDCdownload | 0.000 | 0.001 | 0.001 | |
GDCprepare | 0 | 0 | 0 | |
GDCprepare_clinic | 1.205 | 0.139 | 32.131 | |
GDCquery | 1.711 | 0.054 | 10.325 | |
GDCquery_ATAC_seq | 0.351 | 0.035 | 1.678 | |
GDCquery_clinic | 0.812 | 0.054 | 3.667 | |
PanCancerAtlas_subtypes | 0.014 | 0.002 | 0.017 | |
TCGAVisualize_volcano | 0.368 | 0.017 | 0.389 | |
TCGA_MolecularSubtype | 0.422 | 0.004 | 0.427 | |
TCGAanalyze_DEA | 11.402 | 0.703 | 12.205 | |
TCGAanalyze_DEA_Affy | 0.000 | 0.000 | 0.001 | |
TCGAanalyze_DMC | 1.203 | 0.116 | 1.328 | |
TCGAanalyze_EA | 0 | 0 | 0 | |
TCGAanalyze_EAcomplete | 2.837 | 0.104 | 2.967 | |
TCGAanalyze_Filtering | 4.112 | 0.112 | 4.264 | |
TCGAanalyze_LevelTab | 5.824 | 0.200 | 6.083 | |
TCGAanalyze_Normalization | 2.784 | 0.076 | 2.881 | |
TCGAanalyze_Pathview | 0 | 0 | 0 | |
TCGAanalyze_Stemness | 1.913 | 0.063 | 1.996 | |
TCGAanalyze_SurvivalKM | 0.175 | 0.010 | 0.186 | |
TCGAanalyze_survival | 3.232 | 0.103 | 3.377 | |
TCGAprepare_Affy | 0 | 0 | 0 | |
TCGAquery_MatchedCoupledSampleTypes | 0.003 | 0.001 | 0.003 | |
TCGAquery_SampleTypes | 0.001 | 0.000 | 0.001 | |
TCGAquery_recount2 | 0 | 0 | 0 | |
TCGAquery_subtype | 0.007 | 0.001 | 0.008 | |
TCGAtumor_purity | 0.071 | 0.001 | 0.073 | |
TCGAvisualize_EAbarplot | 2.842 | 0.074 | 2.951 | |
TCGAvisualize_Heatmap | 2.363 | 0.115 | 2.502 | |
TCGAvisualize_PCA | 2.021 | 0.041 | 2.079 | |
TCGAvisualize_meanMethylation | 3.340 | 0.061 | 3.425 | |
TCGAvisualize_oncoprint | 0.000 | 0.000 | 0.001 | |
TCGAvisualize_starburst | 0.000 | 0.000 | 0.001 | |
UseRaw_afterFilter | 0 | 0 | 0 | |
colDataPrepare | 0.128 | 0.006 | 0.621 | |
dmc.non.parametric | 0.113 | 0.017 | 0.132 | |
dmc.non.parametric.se | 0.173 | 0.012 | 0.186 | |
gaiaCNVplot | 0.034 | 0.004 | 0.038 | |
geneInfoHT | 0 | 0 | 0 | |
getAdjacencyBiogrid | 0.001 | 0.000 | 0.002 | |
getDataCategorySummary | 1.346 | 0.051 | 3.122 | |
getGDCInfo | 0.021 | 0.002 | 0.141 | |
getGDCprojects | 0.019 | 0.002 | 0.130 | |
getLinkedOmicsData | 0 | 0 | 0 | |
getMC3MAF | 0 | 0 | 0 | |
getManifest | 10.524 | 0.258 | 100.948 | |
getNbCases | 0 | 0 | 0 | |
getNbFiles | 0 | 0 | 0 | |
getProjectSummary | 0.037 | 0.004 | 0.563 | |
getResults | 0.770 | 0.028 | 7.158 | |
getSampleFilesSummary | 0.486 | 0.029 | 2.001 | |
getTSS | 0.000 | 0.001 | 0.000 | |
gliomaClassifier | 0.000 | 0.001 | 0.001 | |
isServeOK | 0.018 | 0.002 | 0.134 | |
matchedMetExp | 1.040 | 0.051 | 10.093 | |