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This page was generated on 2023-05-31 05:44:45 -0000 (Wed, 31 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4219
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CHECK results for TCGAbiolinks on kunpeng1


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.

raw results

Package 2044/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.29.4  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2023-05-29 10:19:22 -0000 (Mon, 29 May 2023)
git_url: https://git.bioconductor.org/packages/TCGAbiolinks
git_branch: devel
git_last_commit: 6c183034
git_last_commit_date: 2023-05-25 16:34:35 -0000 (Thu, 25 May 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

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

Command output

##############################################################################
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### 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
###
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* 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.



Installation output

TCGAbiolinks.Rcheck/00install.out

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###
### 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)

Tests output

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 

Example timings

TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings

nameusersystemelapsed
GDCdownload000
GDCprepare000
GDCprepare_clinic 3.026 0.34738.950
GDCquery 1.443 0.19614.093
GDCquery_ATAC_seq0.9860.0895.034
GDCquery_clinic 2.118 0.20318.183
PanCancerAtlas_subtypes0.0070.0120.019
TCGAVisualize_volcano0.4090.0600.468
TCGA_MolecularSubtype0.4770.0400.517
TCGAanalyze_DEA14.240 0.75214.993
TCGAanalyze_DEA_Affy000
TCGAanalyze_DMC1.2690.0401.309
TCGAanalyze_EA000
TCGAanalyze_EAcomplete3.2720.1603.432
TCGAanalyze_Filtering4.0090.0524.062
TCGAanalyze_LevelTab7.4200.2207.642
TCGAanalyze_Normalization2.8590.0962.955
TCGAanalyze_Pathview000
TCGAanalyze_Stemness2.0650.0962.160
TCGAanalyze_SurvivalKM0.1890.0230.212
TCGAanalyze_survival3.7010.2443.945
TCGAprepare_Affy000
TCGAquery_MatchedCoupledSampleTypes0.0000.0030.003
TCGAquery_SampleTypes0.0010.0000.001
TCGAquery_recount2000
TCGAquery_subtype0.0090.0000.008
TCGAtumor_purity0.080.000.08
TCGAvisualize_EAbarplot3.2120.1083.320
TCGAvisualize_Heatmap2.5920.0922.685
TCGAvisualize_PCA2.0720.0522.124
TCGAvisualize_meanMethylation3.8470.1003.947
TCGAvisualize_oncoprint000
TCGAvisualize_starburst000
UseRaw_afterFilter0.0010.0000.000
colDataPrepare0.4610.0083.315
dmc.non.parametric0.1460.0160.162
dmc.non.parametric.se0.2410.0120.253
gaiaCNVplot0.0360.0040.041
getAdjacencyBiogrid0.0020.0000.002
getDataCategorySummary1.5660.1647.306
getGDCInfo0.1570.0041.233
getGDCprojects0.1810.0081.167
getLinkedOmicsData000
getMC3MAF000
getManifest12.499 1.03696.221
getNbCases000
getNbFiles0.0010.0000.000
getProjectSummary0.3350.0152.283
getResults 1.630 0.12016.086
getSampleFilesSummary0.8360.0447.800
getTSS000
gliomaClassifier0.0000.0000.001
isServeOK0.1510.0041.213
matchedMetExp 2.926 0.19230.036