Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:45 -0000 (Wed, 31 May 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 2044/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TCGAbiolinks 2.29.4 (landing page) Tiago Chedraoui Silva
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: TCGAbiolinks |
Version: 2.29.4 |
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings TCGAbiolinks_2.29.4.tar.gz |
StartedAt: 2023-05-30 21:08:48 -0000 (Tue, 30 May 2023) |
EndedAt: 2023-05-30 21:29:36 -0000 (Tue, 30 May 2023) |
EllapsedTime: 1247.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TCGAbiolinks.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings TCGAbiolinks_2.29.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/TCGAbiolinks.Rcheck’ * using R version 4.3.0 (2023-04-21) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TCGAbiolinks’ version ‘2.29.4’ * 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 startup messages can be suppressed ... OK * checking dependencies in R code ... OK * 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’ 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 14.240 0.752 14.993 getManifest 12.499 1.036 96.221 TCGAanalyze_LevelTab 7.420 0.220 7.642 GDCprepare_clinic 3.026 0.347 38.950 matchedMetExp 2.926 0.192 30.036 GDCquery_clinic 2.118 0.203 18.183 getResults 1.630 0.120 16.086 getDataCategorySummary 1.566 0.164 7.306 GDCquery 1.443 0.196 14.093 GDCquery_ATAC_seq 0.986 0.089 5.034 getSampleFilesSummary 0.836 0.044 7.800 * 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 ‘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 ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/TCGAbiolinks.Rcheck/00check.log’ for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 0 | SKIP 19 | PASS 32 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • On Bioconductor (19) [ FAIL 0 | WARN 0 | SKIP 19 | PASS 32 ] > > proc.time() user system elapsed 56.662 1.478 58.129
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
name | user | system | elapsed | |
GDCdownload | 0 | 0 | 0 | |
GDCprepare | 0 | 0 | 0 | |
GDCprepare_clinic | 3.026 | 0.347 | 38.950 | |
GDCquery | 1.443 | 0.196 | 14.093 | |
GDCquery_ATAC_seq | 0.986 | 0.089 | 5.034 | |
GDCquery_clinic | 2.118 | 0.203 | 18.183 | |
PanCancerAtlas_subtypes | 0.007 | 0.012 | 0.019 | |
TCGAVisualize_volcano | 0.409 | 0.060 | 0.468 | |
TCGA_MolecularSubtype | 0.477 | 0.040 | 0.517 | |
TCGAanalyze_DEA | 14.240 | 0.752 | 14.993 | |
TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
TCGAanalyze_DMC | 1.269 | 0.040 | 1.309 | |
TCGAanalyze_EA | 0 | 0 | 0 | |
TCGAanalyze_EAcomplete | 3.272 | 0.160 | 3.432 | |
TCGAanalyze_Filtering | 4.009 | 0.052 | 4.062 | |
TCGAanalyze_LevelTab | 7.420 | 0.220 | 7.642 | |
TCGAanalyze_Normalization | 2.859 | 0.096 | 2.955 | |
TCGAanalyze_Pathview | 0 | 0 | 0 | |
TCGAanalyze_Stemness | 2.065 | 0.096 | 2.160 | |
TCGAanalyze_SurvivalKM | 0.189 | 0.023 | 0.212 | |
TCGAanalyze_survival | 3.701 | 0.244 | 3.945 | |
TCGAprepare_Affy | 0 | 0 | 0 | |
TCGAquery_MatchedCoupledSampleTypes | 0.000 | 0.003 | 0.003 | |
TCGAquery_SampleTypes | 0.001 | 0.000 | 0.001 | |
TCGAquery_recount2 | 0 | 0 | 0 | |
TCGAquery_subtype | 0.009 | 0.000 | 0.008 | |
TCGAtumor_purity | 0.08 | 0.00 | 0.08 | |
TCGAvisualize_EAbarplot | 3.212 | 0.108 | 3.320 | |
TCGAvisualize_Heatmap | 2.592 | 0.092 | 2.685 | |
TCGAvisualize_PCA | 2.072 | 0.052 | 2.124 | |
TCGAvisualize_meanMethylation | 3.847 | 0.100 | 3.947 | |
TCGAvisualize_oncoprint | 0 | 0 | 0 | |
TCGAvisualize_starburst | 0 | 0 | 0 | |
UseRaw_afterFilter | 0.001 | 0.000 | 0.000 | |
colDataPrepare | 0.461 | 0.008 | 3.315 | |
dmc.non.parametric | 0.146 | 0.016 | 0.162 | |
dmc.non.parametric.se | 0.241 | 0.012 | 0.253 | |
gaiaCNVplot | 0.036 | 0.004 | 0.041 | |
getAdjacencyBiogrid | 0.002 | 0.000 | 0.002 | |
getDataCategorySummary | 1.566 | 0.164 | 7.306 | |
getGDCInfo | 0.157 | 0.004 | 1.233 | |
getGDCprojects | 0.181 | 0.008 | 1.167 | |
getLinkedOmicsData | 0 | 0 | 0 | |
getMC3MAF | 0 | 0 | 0 | |
getManifest | 12.499 | 1.036 | 96.221 | |
getNbCases | 0 | 0 | 0 | |
getNbFiles | 0.001 | 0.000 | 0.000 | |
getProjectSummary | 0.335 | 0.015 | 2.283 | |
getResults | 1.630 | 0.120 | 16.086 | |
getSampleFilesSummary | 0.836 | 0.044 | 7.800 | |
getTSS | 0 | 0 | 0 | |
gliomaClassifier | 0.000 | 0.000 | 0.001 | |
isServeOK | 0.151 | 0.004 | 1.213 | |
matchedMetExp | 2.926 | 0.192 | 30.036 | |