Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:21 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 2027/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TCGAbiolinks 2.26.0 (landing page) Tiago Chedraoui Silva
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: TCGAbiolinks |
Version: 2.26.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TCGAbiolinks_2.26.0.tar.gz |
StartedAt: 2023-04-11 00:29:59 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 01:09:59 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 2400.0 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: TCGAbiolinks.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TCGAbiolinks_2.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/TCGAbiolinks.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TCGAbiolinks’ version ‘2.26.0’ * 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 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 loading without being on the library search path ... OK * checking dependencies in R code ... WARNING 'library' or 'require' call not declared from: ‘dplyr’ 'library' or 'require' calls in package code: ‘dplyr’ ‘maftools’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * 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’ 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’ colDataPrepare: no visible binding for global variable ‘sample_type’ 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’ readSingleCellAnalysis : <anonymous>: no visible global function definition for ‘Read10X’ Undefined global functions or variables: Read10X Tumor.purity assay.list barcode bcr_patient_barcode clinical coordinates days_to_last_followup exon geFDR2 gene_name is_ffpe logFC meFDR2 rse_gene sample_submitter_id sample_type 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 GDCquery_clinic 685.271 6.921 723.523 getManifest 11.952 1.465 82.849 TCGAanalyze_DEA 9.977 0.180 10.158 TCGAanalyze_LevelTab 5.503 0.016 5.519 GDCdownload 2.449 0.206 34.803 GDCprepare_clinic 2.374 0.109 56.458 matchedMetExp 0.813 0.080 5.608 getResults 0.657 0.052 5.748 GDCquery 0.543 0.004 5.724 * 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 ... ‘analysis.Rmd’ using ‘UTF-8’... OK ‘casestudy.Rmd’ using ‘UTF-8’... OK ‘classifiers.Rmd’ using ‘UTF-8’... OK ‘clinical.Rmd’ using ‘UTF-8’... OK ‘download_prepare.Rmd’ using ‘UTF-8’... OK ‘extension.Rmd’ using ‘UTF-8’... OK ‘gui.Rmd’ using ‘UTF-8’... OK ‘index.Rmd’ using ‘UTF-8’... OK ‘mutation.Rmd’ using ‘UTF-8’... OK ‘query.Rmd’ using ‘UTF-8’... OK ‘stemness_score.Rmd’ using ‘UTF-8’... OK ‘subtypes.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ...
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 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" [ FAIL 0 | WARN 901 | SKIP 22 | PASS 45 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • On Bioconductor (22) [ FAIL 0 | WARN 901 | SKIP 22 | PASS 45 ] > > proc.time() user system elapsed 146.965 5.552 159.761
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
name | user | system | elapsed | |
GDCdownload | 2.449 | 0.206 | 34.803 | |
GDCprepare | 0 | 0 | 0 | |
GDCprepare_clinic | 2.374 | 0.109 | 56.458 | |
GDCquery | 0.543 | 0.004 | 5.724 | |
GDCquery_ATAC_seq | 0.329 | 0.029 | 0.754 | |
GDCquery_clinic | 685.271 | 6.921 | 723.523 | |
PanCancerAtlas_subtypes | 0.015 | 0.000 | 0.014 | |
TCGAVisualize_volcano | 0.494 | 0.004 | 0.498 | |
TCGA_MolecularSubtype | 0.274 | 0.000 | 0.274 | |
TCGAanalyze_DEA | 9.977 | 0.180 | 10.158 | |
TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
TCGAanalyze_DMC | 0.950 | 0.024 | 0.975 | |
TCGAanalyze_EA | 0 | 0 | 0 | |
TCGAanalyze_EAcomplete | 2.27 | 0.08 | 2.35 | |
TCGAanalyze_Filtering | 3.203 | 0.007 | 3.210 | |
TCGAanalyze_LevelTab | 5.503 | 0.016 | 5.519 | |
TCGAanalyze_Normalization | 1.607 | 0.000 | 1.606 | |
TCGAanalyze_Pathview | 0.001 | 0.000 | 0.000 | |
TCGAanalyze_Stemness | 1.731 | 0.004 | 1.735 | |
TCGAanalyze_SurvivalKM | 0.1 | 0.0 | 0.1 | |
TCGAanalyze_survival | 2.734 | 0.060 | 2.794 | |
TCGAprepare_Affy | 0 | 0 | 0 | |
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 | 0.06 | 0.00 | 0.06 | |
TCGAvisualize_EAbarplot | 2.171 | 0.008 | 2.179 | |
TCGAvisualize_Heatmap | 1.766 | 0.004 | 1.770 | |
TCGAvisualize_PCA | 1.981 | 0.012 | 1.992 | |
TCGAvisualize_meanMethylation | 2.881 | 0.004 | 2.885 | |
TCGAvisualize_oncoprint | 0 | 0 | 0 | |
TCGAvisualize_starburst | 0.001 | 0.000 | 0.001 | |
UseRaw_afterFilter | 0 | 0 | 0 | |
colDataPrepare | 0.138 | 0.004 | 0.828 | |
dmc.non.parametric | 0.090 | 0.008 | 0.097 | |
dmc.non.parametric.se | 0.193 | 0.000 | 0.193 | |
gaiaCNVplot | 0.043 | 0.000 | 0.043 | |
getAdjacencyBiogrid | 0.002 | 0.000 | 0.002 | |
getDataCategorySummary | 1.155 | 0.016 | 4.611 | |
getGDCInfo | 0.024 | 0.012 | 0.154 | |
getGDCprojects | 0.057 | 0.024 | 0.193 | |
getLinkedOmicsData | 0.001 | 0.000 | 0.001 | |
getMC3MAF | 0 | 0 | 0 | |
getManifest | 11.952 | 1.465 | 82.849 | |
getNbCases | 0 | 0 | 0 | |
getNbFiles | 0 | 0 | 0 | |
getProjectSummary | 0.071 | 0.005 | 0.326 | |
getResults | 0.657 | 0.052 | 5.748 | |
getSampleFilesSummary | 0.535 | 0.096 | 2.093 | |
getTSS | 0 | 0 | 0 | |
gliomaClassifier | 0 | 0 | 0 | |
isServeOK | 0.026 | 0.000 | 0.158 | |
matchedMetExp | 0.813 | 0.080 | 5.608 | |