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This page was generated on 2025-08-15 12:12 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 2146/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.37.1  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 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
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  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: 2025-08-15 11:55:13 -0000 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 12:08:15 -0000 (Fri, 15 Aug 2025)
EllapsedTime: 781.7 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        12.911  1.140  14.089
getManifest            11.222  0.589 151.042
TCGAanalyze_LevelTab    6.449  0.188   6.654
GDCprepare_clinic       2.168  0.279  57.311
getDataCategorySummary  2.196  0.126  10.816
matchedMetExp           1.375  0.379  36.768
GDCquery_clinic         1.196  0.484  18.488
getResults              1.599  0.071  31.588
GDCquery                1.186  0.172  23.364
getSampleFilesSummary   0.613  0.028  17.108
GDCquery_ATAC_seq       0.399  0.082   5.687
getProjectSummary       0.051  0.004   6.390
* 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 
 51.838   1.457  53.401 

Example timings

TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings

nameusersystemelapsed
GDCdownload000
GDCprepare000
GDCprepare_clinic 2.168 0.27957.311
GDCquery 1.186 0.17223.364
GDCquery_ATAC_seq0.3990.0825.687
GDCquery_clinic 1.196 0.48418.488
PanCancerAtlas_subtypes0.0120.0120.024
TCGAVisualize_volcano0.4990.1670.685
TCGA_MolecularSubtype0.4680.0280.497
TCGAanalyze_DEA12.911 1.14014.089
TCGAanalyze_DEA_Affy000
TCGAanalyze_DMC1.4090.0841.498
TCGAanalyze_EA000
TCGAanalyze_EAcomplete2.9360.1483.093
TCGAanalyze_Filtering3.5310.0473.590
TCGAanalyze_LevelTab6.4490.1886.654
TCGAanalyze_Normalization1.7000.0151.720
TCGAanalyze_Pathview000
TCGAanalyze_Stemness2.0990.0122.118
TCGAanalyze_SurvivalKM0.1930.0160.210
TCGAanalyze_survival3.5650.1003.695
TCGAprepare_Affy000
TCGAquery_MatchedCoupledSampleTypes0.0000.0030.003
TCGAquery_SampleTypes0.0020.0000.002
TCGAquery_recount2000
TCGAquery_subtype0.0070.0000.007
TCGAtumor_purity0.0710.0000.072
TCGAvisualize_EAbarplot2.8220.0322.864
TCGAvisualize_Heatmap2.6320.1082.748
TCGAvisualize_PCA2.0930.0312.133
TCGAvisualize_meanMethylation4.1430.1044.261
TCGAvisualize_oncoprint0.0010.0000.000
TCGAvisualize_starburst000
UseRaw_afterFilter000
colDataPrepare0.2400.0003.498
dmc.non.parametric0.1370.0080.145
dmc.non.parametric.se0.2260.0160.243
gaiaCNVplot0.0360.0040.040
geneInfoHT0.0000.0000.001
getAdjacencyBiogrid0.0020.0000.002
getDataCategorySummary 2.196 0.12610.816
getGDCInfo0.0260.0041.190
getGDCprojects0.0300.0010.746
getLinkedOmicsData000
getMC3MAF0.0000.0000.001
getManifest 11.222 0.589151.042
getNbCases000
getNbFiles0.0000.0000.001
getProjectSummary0.0510.0046.390
getResults 1.599 0.07131.588
getSampleFilesSummary 0.613 0.02817.108
getTSS000
gliomaClassifier000
isServeOK0.0250.0001.169
matchedMetExp 1.375 0.37936.768