Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-09-24 22:55 -0400 (Tue, 24 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4760 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4497 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4526 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4475 |
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 | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings TCGAbiolinks_2.32.0.tar.gz |
StartedAt: 2024-09-23 04:24:28 -0400 (Mon, 23 Sep 2024) |
EndedAt: 2024-09-23 04:38:47 -0400 (Mon, 23 Sep 2024) |
EllapsedTime: 859.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TCGAbiolinks.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings TCGAbiolinks_2.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/TCGAbiolinks.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 6.3Mb 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 : <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 9.620 0.646 10.268 getManifest 6.998 0.094 95.146 TCGAanalyze_LevelTab 5.018 0.247 5.265 GDCquery 1.825 0.325 10.022 matchedMetExp 1.538 0.181 9.760 GDCprepare_clinic 1.417 0.178 30.744 GDCquery_clinic 1.165 0.079 5.101 getResults 0.929 0.081 6.523 * 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/TCGAbiolinks.Rcheck/00check.log’ for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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 41.452 1.413 42.856
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
name | user | system | elapsed | |
GDCdownload | 0.001 | 0.000 | 0.000 | |
GDCprepare | 0 | 0 | 0 | |
GDCprepare_clinic | 1.417 | 0.178 | 30.744 | |
GDCquery | 1.825 | 0.325 | 10.022 | |
GDCquery_ATAC_seq | 0.523 | 0.053 | 1.566 | |
GDCquery_clinic | 1.165 | 0.079 | 5.101 | |
PanCancerAtlas_subtypes | 0.008 | 0.008 | 0.016 | |
TCGAVisualize_volcano | 0.277 | 0.024 | 0.302 | |
TCGA_MolecularSubtype | 0.288 | 0.016 | 0.304 | |
TCGAanalyze_DEA | 9.620 | 0.646 | 10.268 | |
TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
TCGAanalyze_DMC | 0.893 | 0.132 | 1.026 | |
TCGAanalyze_EA | 0 | 0 | 0 | |
TCGAanalyze_EAcomplete | 2.120 | 0.047 | 2.168 | |
TCGAanalyze_Filtering | 3.155 | 0.060 | 3.214 | |
TCGAanalyze_LevelTab | 5.018 | 0.247 | 5.265 | |
TCGAanalyze_Normalization | 1.313 | 0.004 | 1.317 | |
TCGAanalyze_Pathview | 0 | 0 | 0 | |
TCGAanalyze_Stemness | 1.543 | 0.024 | 1.568 | |
TCGAanalyze_SurvivalKM | 0.131 | 0.008 | 0.139 | |
TCGAanalyze_survival | 2.231 | 0.076 | 2.307 | |
TCGAprepare_Affy | 0 | 0 | 0 | |
TCGAquery_MatchedCoupledSampleTypes | 0.003 | 0.000 | 0.002 | |
TCGAquery_SampleTypes | 0.001 | 0.000 | 0.001 | |
TCGAquery_recount2 | 0 | 0 | 0 | |
TCGAquery_subtype | 0.004 | 0.003 | 0.007 | |
TCGAtumor_purity | 0.055 | 0.004 | 0.059 | |
TCGAvisualize_EAbarplot | 2.044 | 0.052 | 2.096 | |
TCGAvisualize_Heatmap | 1.735 | 0.020 | 1.755 | |
TCGAvisualize_PCA | 2.554 | 0.208 | 2.762 | |
TCGAvisualize_meanMethylation | 2.494 | 0.068 | 2.562 | |
TCGAvisualize_oncoprint | 0.001 | 0.000 | 0.001 | |
TCGAvisualize_starburst | 0.001 | 0.000 | 0.001 | |
UseRaw_afterFilter | 0 | 0 | 0 | |
colDataPrepare | 0.258 | 0.000 | 0.756 | |
dmc.non.parametric | 0.093 | 0.016 | 0.109 | |
dmc.non.parametric.se | 0.137 | 0.016 | 0.153 | |
gaiaCNVplot | 0.022 | 0.004 | 0.027 | |
geneInfoHT | 0.001 | 0.000 | 0.001 | |
getAdjacencyBiogrid | 0.002 | 0.000 | 0.002 | |
getDataCategorySummary | 0.889 | 0.012 | 2.511 | |
getGDCInfo | 0.059 | 0.004 | 0.201 | |
getGDCprojects | 0.098 | 0.000 | 0.249 | |
getLinkedOmicsData | 0.001 | 0.000 | 0.001 | |
getMC3MAF | 0.001 | 0.000 | 0.000 | |
getManifest | 6.998 | 0.094 | 95.146 | |
getNbCases | 0 | 0 | 0 | |
getNbFiles | 0.001 | 0.000 | 0.000 | |
getProjectSummary | 0.158 | 0.004 | 0.638 | |
getResults | 0.929 | 0.081 | 6.523 | |
getSampleFilesSummary | 0.616 | 0.060 | 2.173 | |
getTSS | 0 | 0 | 0 | |
gliomaClassifier | 0 | 0 | 0 | |
isServeOK | 0.061 | 0.007 | 0.203 | |
matchedMetExp | 1.538 | 0.181 | 9.760 | |