Tiago Chedraoui Silva
| Snapshot Date: 2025-11-05 13:40 -0500 (Wed, 05 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/TCGAbiolinks |
| git_branch: devel |
| git_last_commit: 2072af1 |
| git_last_commit_date: 2025-10-29 10:27:16 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-06 11:32 -0500 (Thu, 06 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| 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 2156/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.39.0 (landing page) Tiago Chedraoui Silva
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
|
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. |
| Package: TCGAbiolinks |
| Version: 2.39.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings TCGAbiolinks_2.39.0.tar.gz |
| StartedAt: 2025-11-06 04:37:46 -0500 (Thu, 06 Nov 2025) |
| EndedAt: 2025-11-06 04:54:24 -0500 (Thu, 06 Nov 2025) |
| EllapsedTime: 997.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: 2 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings TCGAbiolinks_2.39.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/TCGAbiolinks.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.39.0’
* 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 6.3Mb
sub-directories of 1Mb or more:
R 1.6Mb
data 4.3Mb
* 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 11.658 0.978 12.640
getManifest 7.836 0.138 129.063
GDCprepare_clinic 1.502 0.206 43.211
getResults 1.448 0.070 16.679
matchedMetExp 1.353 0.065 12.056
GDCquery 1.018 0.045 11.460
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘TCGAbiolinks’ ... ** this is package ‘TCGAbiolinks’ version ‘2.39.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 31 ]
══ 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 31 ]
>
> proc.time()
user system elapsed
44.601 1.526 46.121
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 0.000 | 0.000 | 0.001 | |
| GDCprepare | 0 | 0 | 0 | |
| GDCprepare_clinic | 1.502 | 0.206 | 43.211 | |
| GDCquery | 1.018 | 0.045 | 11.460 | |
| GDCquery_ATAC_seq | 0.479 | 0.040 | 1.695 | |
| GDCquery_clinic | 1.213 | 0.093 | 4.575 | |
| PanCancerAtlas_subtypes | 0.015 | 0.002 | 0.017 | |
| TCGAVisualize_volcano | 0.430 | 0.048 | 0.477 | |
| TCGA_MolecularSubtype | 0.343 | 0.020 | 0.363 | |
| TCGAanalyze_DEA | 11.658 | 0.978 | 12.640 | |
| TCGAanalyze_DEA_Affy | 0.000 | 0.000 | 0.001 | |
| TCGAanalyze_DMC | 1.336 | 0.088 | 1.425 | |
| TCGAanalyze_EA | 0.000 | 0.000 | 0.001 | |
| TCGAanalyze_EAcomplete | 1.967 | 0.153 | 2.120 | |
| TCGAanalyze_Filtering | 2.818 | 0.094 | 2.913 | |
| TCGAanalyze_LevelTab | 4.008 | 0.081 | 4.089 | |
| TCGAanalyze_Normalization | 2.250 | 0.224 | 2.474 | |
| TCGAanalyze_Pathview | 0.000 | 0.000 | 0.001 | |
| TCGAanalyze_Stemness | 1.369 | 0.034 | 1.403 | |
| TCGAanalyze_SurvivalKM | 0.140 | 0.010 | 0.149 | |
| TCGAanalyze_survival | 3.739 | 0.111 | 3.850 | |
| TCGAprepare_Affy | 0.000 | 0.000 | 0.001 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.003 | 0.000 | 0.003 | |
| TCGAquery_SampleTypes | 0.001 | 0.000 | 0.002 | |
| TCGAquery_recount2 | 0 | 0 | 0 | |
| TCGAquery_subtype | 0.007 | 0.001 | 0.007 | |
| TCGAtumor_purity | 0.052 | 0.004 | 0.056 | |
| TCGAvisualize_EAbarplot | 1.875 | 0.036 | 1.911 | |
| TCGAvisualize_Heatmap | 1.885 | 0.050 | 1.936 | |
| TCGAvisualize_PCA | 1.738 | 0.101 | 1.839 | |
| TCGAvisualize_meanMethylation | 4.369 | 0.127 | 4.496 | |
| TCGAvisualize_oncoprint | 0.000 | 0.000 | 0.001 | |
| TCGAvisualize_starburst | 0.001 | 0.000 | 0.001 | |
| UseRaw_afterFilter | 0 | 0 | 0 | |
| colDataPrepare | 0.299 | 0.011 | 0.949 | |
| dmc.non.parametric | 0.107 | 0.021 | 0.127 | |
| dmc.non.parametric.se | 0.183 | 0.013 | 0.195 | |
| gaiaCNVplot | 0.027 | 0.000 | 0.026 | |
| geneInfoHT | 0.000 | 0.001 | 0.001 | |
| getAdjacencyBiogrid | 0.002 | 0.000 | 0.002 | |
| getDataCategorySummary | 1.434 | 0.022 | 4.277 | |
| getGDCInfo | 0.049 | 0.001 | 0.306 | |
| getGDCprojects | 0.068 | 0.004 | 0.259 | |
| getLinkedOmicsData | 0 | 0 | 0 | |
| getMC3MAF | 0 | 0 | 0 | |
| getManifest | 7.836 | 0.138 | 129.063 | |
| getNbCases | 0 | 0 | 0 | |
| getNbFiles | 0 | 0 | 0 | |
| getProjectSummary | 0.162 | 0.026 | 0.559 | |
| getResults | 1.448 | 0.070 | 16.679 | |
| getSampleFilesSummary | 0.575 | 0.012 | 2.508 | |
| getTSS | 0.001 | 0.000 | 0.001 | |
| gliomaClassifier | 0.001 | 0.000 | 0.000 | |
| isServeOK | 0.050 | 0.009 | 0.137 | |
| matchedMetExp | 1.353 | 0.065 | 12.056 | |