Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-25 12:05 -0500 (Mon, 25 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4528 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4441 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4465 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4460 |
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 2123/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TCGAbiolinks 2.34.0 (landing page) Tiago Chedraoui Silva
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | 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: 2.34.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAbiolinks.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.34.0.tar.gz |
StartedAt: 2024-11-21 06:11:07 -0500 (Thu, 21 Nov 2024) |
EndedAt: 2024-11-21 06:21:10 -0500 (Thu, 21 Nov 2024) |
EllapsedTime: 602.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TCGAbiolinks.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAbiolinks.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/TCGAbiolinks.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'TCGAbiolinks/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'TCGAbiolinks' version '2.34.0' * 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 whether package 'TCGAbiolinks' can be installed ... OK * checking installed package size ... NOTE 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 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 13.03 0.59 13.63 getManifest 9.42 0.21 97.00 TCGAanalyze_LevelTab 7.27 0.17 7.44 TCGAanalyze_Filtering 5.00 0.09 5.09 GDCprepare_clinic 1.26 0.14 32.72 GDCquery 1.25 0.00 9.44 matchedMetExp 0.78 0.01 9.33 getResults 0.73 0.04 7.64 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/TCGAbiolinks.Rcheck/00check.log' for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 58.81 2.75 61.89
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
name | user | system | elapsed | |
GDCdownload | 0 | 0 | 0 | |
GDCprepare | 0 | 0 | 0 | |
GDCprepare_clinic | 1.26 | 0.14 | 32.72 | |
GDCquery | 1.25 | 0.00 | 9.44 | |
GDCquery_ATAC_seq | 1.25 | 0.09 | 2.34 | |
GDCquery_clinic | 0.83 | 0.03 | 4.20 | |
PanCancerAtlas_subtypes | 0.02 | 0.02 | 0.04 | |
TCGAVisualize_volcano | 0.40 | 0.08 | 0.78 | |
TCGA_MolecularSubtype | 0.30 | 0.00 | 0.29 | |
TCGAanalyze_DEA | 13.03 | 0.59 | 13.63 | |
TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
TCGAanalyze_DMC | 1.56 | 0.14 | 1.70 | |
TCGAanalyze_EA | 0 | 0 | 0 | |
TCGAanalyze_EAcomplete | 3.75 | 0.13 | 3.88 | |
TCGAanalyze_Filtering | 5.00 | 0.09 | 5.09 | |
TCGAanalyze_LevelTab | 7.27 | 0.17 | 7.44 | |
TCGAanalyze_Normalization | 2.23 | 0.03 | 2.26 | |
TCGAanalyze_Pathview | 0 | 0 | 0 | |
TCGAanalyze_Stemness | 3.32 | 0.00 | 3.32 | |
TCGAanalyze_SurvivalKM | 0.14 | 0.03 | 0.17 | |
TCGAanalyze_survival | 3.42 | 0.18 | 3.81 | |
TCGAprepare_Affy | 0 | 0 | 0 | |
TCGAquery_MatchedCoupledSampleTypes | 0 | 0 | 0 | |
TCGAquery_SampleTypes | 0.00 | 0.01 | 0.02 | |
TCGAquery_recount2 | 0 | 0 | 0 | |
TCGAquery_subtype | 0 | 0 | 0 | |
TCGAtumor_purity | 0.09 | 0.02 | 0.11 | |
TCGAvisualize_EAbarplot | 3.34 | 0.11 | 3.45 | |
TCGAvisualize_Heatmap | 3.27 | 1.03 | 3.27 | |
TCGAvisualize_PCA | 2.57 | 0.11 | 2.73 | |
TCGAvisualize_meanMethylation | 4.61 | 0.07 | 4.69 | |
TCGAvisualize_oncoprint | 0 | 0 | 0 | |
TCGAvisualize_starburst | 0 | 0 | 0 | |
UseRaw_afterFilter | 0 | 0 | 0 | |
colDataPrepare | 0.11 | 0.00 | 0.67 | |
dmc.non.parametric | 0.16 | 0.02 | 0.18 | |
dmc.non.parametric.se | 0.30 | 0.00 | 0.29 | |
gaiaCNVplot | 0.04 | 0.00 | 0.05 | |
geneInfoHT | 0 | 0 | 0 | |
getAdjacencyBiogrid | 0 | 0 | 0 | |
getDataCategorySummary | 1.02 | 0.02 | 2.36 | |
getGDCInfo | 0.00 | 0.00 | 0.16 | |
getGDCprojects | 0.03 | 0.00 | 0.15 | |
getLinkedOmicsData | 0 | 0 | 0 | |
getMC3MAF | 0 | 0 | 0 | |
getManifest | 9.42 | 0.21 | 97.00 | |
getNbCases | 0 | 0 | 0 | |
getNbFiles | 0 | 0 | 0 | |
getProjectSummary | 0.05 | 0.00 | 0.35 | |
getResults | 0.73 | 0.04 | 7.64 | |
getSampleFilesSummary | 1.93 | 0.01 | 2.95 | |
getTSS | 0 | 0 | 0 | |
gliomaClassifier | 0 | 0 | 0 | |
isServeOK | 0.00 | 0.00 | 0.16 | |
matchedMetExp | 0.78 | 0.01 | 9.33 | |