Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-04 12:04 -0400 (Thu, 04 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4617 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4564 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 2150/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TCGAbiolinks 2.37.1 (landing page) Tiago Chedraoui Silva
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 2.37.1 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings TCGAbiolinks_2.37.1.tar.gz |
StartedAt: 2025-09-04 05:00:36 -0400 (Thu, 04 Sep 2025) |
EndedAt: 2025-09-04 05:19:46 -0400 (Thu, 04 Sep 2025) |
EllapsedTime: 1150.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TCGAbiolinks.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings TCGAbiolinks_2.37.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/TCGAbiolinks.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TCGAbiolinks’ version ‘2.37.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 23 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... INFO installed size is 6.2Mb sub-directories of 1Mb or more: R 1.6Mb data 4.3Mb * 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 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: no visible binding for global variable ‘submitter_id’ GDCquery_clinic: no visible binding for global variable ‘days_to_follow_up’ GDCquery_clinic: no visible binding for global variable ‘disease_response’ GDCquery_clinic: no visible global function definition for ‘across’ GDCquery_clinic: no visible global function definition for ‘everything’ 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_SurvivalCoxNET: no visible global function definition for ‘colorRampPalette’ TCGAvisualize_SurvivalCoxNET: no visible global function definition for ‘adjustcolor’ 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’ getBarcodeInfo: no visible binding for global variable ‘days_to_follow_up’ getBarcodeInfo: no visible binding for global variable ‘disease_response’ 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 adjustcolor assay.list barcode bcr_patient_barcode clinical colorRampPalette coordinates days_to_follow_up days_to_last_followup disease_response everything exon geFDR2 gene_name is_ffpe logFC meFDR2 rse_gene sample_submitter_id starburst.status submitter_id threshold.starburst value vital_status Consider adding importFrom("grDevices", "adjustcolor", "colorRampPalette") 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 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 9.936 0.673 10.609 getManifest 7.806 0.498 217.627 GDCprepare_clinic 2.198 1.006 44.374 matchedMetExp 1.665 0.097 19.171 getResults 1.294 0.076 28.108 GDCquery_clinic 1.238 0.056 18.547 GDCquery 1.078 0.123 17.677 getSampleFilesSummary 0.592 0.028 15.611 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/TCGAbiolinks.Rcheck/00check.log’ for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘TCGAbiolinks’ ... ** this is package ‘TCGAbiolinks’ version ‘2.37.1’ ** 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 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 38.440 1.204 39.637
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
name | user | system | elapsed | |
GDCdownload | 0 | 0 | 0 | |
GDCprepare | 0.000 | 0.000 | 0.001 | |
GDCprepare_clinic | 2.198 | 1.006 | 44.374 | |
GDCquery | 1.078 | 0.123 | 17.677 | |
GDCquery_ATAC_seq | 0.524 | 0.054 | 1.959 | |
GDCquery_clinic | 1.238 | 0.056 | 18.547 | |
PanCancerAtlas_subtypes | 0.016 | 0.010 | 0.025 | |
TCGAVisualize_volcano | 0.333 | 0.060 | 0.394 | |
TCGA_MolecularSubtype | 0.289 | 0.013 | 0.302 | |
TCGAanalyze_DEA | 9.936 | 0.673 | 10.609 | |
TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
TCGAanalyze_DMC | 0.928 | 0.060 | 0.988 | |
TCGAanalyze_EA | 0.001 | 0.000 | 0.001 | |
TCGAanalyze_EAcomplete | 1.888 | 0.091 | 1.979 | |
TCGAanalyze_Filtering | 2.558 | 0.085 | 2.643 | |
TCGAanalyze_LevelTab | 3.767 | 0.050 | 3.817 | |
TCGAanalyze_Normalization | 1.268 | 0.001 | 1.269 | |
TCGAanalyze_Pathview | 0 | 0 | 0 | |
TCGAanalyze_Stemness | 2.415 | 0.106 | 2.521 | |
TCGAanalyze_SurvivalKM | 0.128 | 0.002 | 0.131 | |
TCGAanalyze_survival | 2.496 | 0.034 | 2.531 | |
TCGAprepare_Affy | 0 | 0 | 0 | |
TCGAquery_MatchedCoupledSampleTypes | 0.001 | 0.001 | 0.003 | |
TCGAquery_SampleTypes | 0.001 | 0.000 | 0.001 | |
TCGAquery_recount2 | 0 | 0 | 0 | |
TCGAquery_subtype | 0.007 | 0.000 | 0.007 | |
TCGAtumor_purity | 0.048 | 0.000 | 0.049 | |
TCGAvisualize_EAbarplot | 1.827 | 0.014 | 1.841 | |
TCGAvisualize_Heatmap | 1.819 | 0.045 | 1.864 | |
TCGAvisualize_PCA | 1.375 | 0.039 | 1.414 | |
TCGAvisualize_meanMethylation | 2.681 | 0.051 | 2.731 | |
TCGAvisualize_oncoprint | 0 | 0 | 0 | |
TCGAvisualize_starburst | 0.000 | 0.000 | 0.001 | |
UseRaw_afterFilter | 0 | 0 | 0 | |
colDataPrepare | 0.301 | 0.024 | 1.052 | |
dmc.non.parametric | 0.093 | 0.006 | 0.099 | |
dmc.non.parametric.se | 0.158 | 0.010 | 0.168 | |
gaiaCNVplot | 0.024 | 0.004 | 0.028 | |
geneInfoHT | 0 | 0 | 0 | |
getAdjacencyBiogrid | 0.001 | 0.000 | 0.002 | |
getDataCategorySummary | 1.605 | 0.093 | 4.241 | |
getGDCInfo | 0.061 | 0.008 | 3.521 | |
getGDCprojects | 0.111 | 0.011 | 0.377 | |
getLinkedOmicsData | 0 | 0 | 0 | |
getMC3MAF | 0 | 0 | 0 | |
getManifest | 7.806 | 0.498 | 217.627 | |
getNbCases | 0 | 0 | 0 | |
getNbFiles | 0 | 0 | 0 | |
getProjectSummary | 0.113 | 0.016 | 3.620 | |
getResults | 1.294 | 0.076 | 28.108 | |
getSampleFilesSummary | 0.592 | 0.028 | 15.611 | |
getTSS | 0 | 0 | 0 | |
gliomaClassifier | 0.000 | 0.000 | 0.001 | |
isServeOK | 0.050 | 0.003 | 0.152 | |
matchedMetExp | 1.665 | 0.097 | 19.171 | |