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This page was generated on 2025-09-01 12:08 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 2149/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.37.1  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 2025)
git_url: https://git.bioconductor.org/packages/TCGAbiolinks
git_branch: devel
git_last_commit: 2cea937
git_last_commit_date: 2025-06-20 09:26:48 -0400 (Fri, 20 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for TCGAbiolinks on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: TCGAbiolinks
Version: 2.37.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TCGAbiolinks_2.37.1.tar.gz
StartedAt: 2025-08-29 12:16:07 -0000 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 12:30:12 -0000 (Fri, 29 Aug 2025)
EllapsedTime: 844.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TCGAbiolinks.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TCGAbiolinks_2.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.37.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... INFO
  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 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: no visible binding for global variable ‘submitter_id’
GDCquery_clinic: no visible binding for global variable
  ‘days_to_follow_up’
GDCquery_clinic: no visible binding for global variable
  ‘disease_response’
GDCquery_clinic: no visible global function definition for ‘across’
GDCquery_clinic: no visible global function definition for ‘everything’
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_SurvivalCoxNET: no visible global function definition for
  ‘colorRampPalette’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
  ‘adjustcolor’
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’
getBarcodeInfo: no visible binding for global variable
  ‘days_to_follow_up’
getBarcodeInfo: no visible binding for global variable
  ‘disease_response’
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 adjustcolor assay.list barcode
  bcr_patient_barcode clinical colorRampPalette coordinates
  days_to_follow_up days_to_last_followup disease_response everything
  exon geFDR2 gene_name is_ffpe logFC meFDR2 rse_gene
  sample_submitter_id starburst.status submitter_id threshold.starburst
  value vital_status
Consider adding
  importFrom("grDevices", "adjustcolor", "colorRampPalette")
to your NAMESPACE file.
* 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        11.857  0.546  12.436
getManifest            11.574  0.422 153.362
TCGAanalyze_LevelTab    5.291  0.039   5.344
GDCprepare_clinic       2.014  1.045  57.656
getDataCategorySummary  2.148  0.053   9.144
getSampleFilesSummary   1.733  0.140   9.664
getResults              1.664  0.112  99.775
GDCquery_clinic         1.229  0.050  16.584
matchedMetExp           1.202  0.048  41.921
GDCquery                1.143  0.051  20.603
GDCquery_ATAC_seq       0.402  0.025   5.329
getProjectSummary       0.056  0.001  11.672
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.


Installation output

TCGAbiolinks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL TCGAbiolinks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘TCGAbiolinks’ ...
** this is package ‘TCGAbiolinks’ version ‘2.37.1’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 52.035   1.450  53.660 

Example timings

TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings

nameusersystemelapsed
GDCdownload0.0010.0000.000
GDCprepare0.0000.0000.001
GDCprepare_clinic 2.014 1.04557.656
GDCquery 1.143 0.05120.603
GDCquery_ATAC_seq0.4020.0255.329
GDCquery_clinic 1.229 0.05016.584
PanCancerAtlas_subtypes0.0140.0000.014
TCGAVisualize_volcano0.4740.0110.491
TCGA_MolecularSubtype0.4520.0000.453
TCGAanalyze_DEA11.857 0.54612.436
TCGAanalyze_DEA_Affy000
TCGAanalyze_DMC1.3490.0961.449
TCGAanalyze_EA0.0010.0000.000
TCGAanalyze_EAcomplete3.6320.1323.772
TCGAanalyze_Filtering3.7130.1153.838
TCGAanalyze_LevelTab5.2910.0395.344
TCGAanalyze_Normalization1.4320.0081.445
TCGAanalyze_Pathview000
TCGAanalyze_Stemness1.8300.0201.855
TCGAanalyze_SurvivalKM0.1950.0240.220
TCGAanalyze_survival3.6580.1043.776
TCGAprepare_Affy000
TCGAquery_MatchedCoupledSampleTypes0.0000.0030.003
TCGAquery_SampleTypes0.0020.0010.001
TCGAquery_recount2000
TCGAquery_subtype0.0070.0000.008
TCGAtumor_purity0.1170.0000.118
TCGAvisualize_EAbarplot2.9080.0552.972
TCGAvisualize_Heatmap2.6690.0282.706
TCGAvisualize_PCA2.1550.0282.190
TCGAvisualize_meanMethylation4.0590.1364.207
TCGAvisualize_oncoprint000
TCGAvisualize_starburst000
UseRaw_afterFilter000
colDataPrepare0.2200.0072.861
dmc.non.parametric0.1400.0040.145
dmc.non.parametric.se0.2250.0080.234
gaiaCNVplot0.0330.0040.037
geneInfoHT000
getAdjacencyBiogrid0.0010.0000.001
getDataCategorySummary2.1480.0539.144
getGDCInfo0.0250.0041.050
getGDCprojects0.0280.0000.743
getLinkedOmicsData0.0010.0000.001
getMC3MAF000
getManifest 11.574 0.422153.362
getNbCases000
getNbFiles000
getProjectSummary 0.056 0.00111.672
getResults 1.664 0.11299.775
getSampleFilesSummary1.7330.1409.664
getTSS000
gliomaClassifier000
isServeOK0.0250.0001.054
matchedMetExp 1.202 0.04841.921