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This page was generated on 2024-02-28 11:37:10 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4671
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4411
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4438
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4414
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 2094/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.31.3  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2024-02-26 14:39:26 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/TCGAbiolinks
git_branch: devel
git_last_commit: b596b1f2
git_last_commit_date: 2024-01-30 20:07:53 -0500 (Tue, 30 Jan 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for TCGAbiolinks on nebbiolo1


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.

raw results


Summary

Package: TCGAbiolinks
Version: 2.31.3
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings TCGAbiolinks_2.31.3.tar.gz
StartedAt: 2024-02-27 03:24:15 -0500 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 03:39:05 -0500 (Tue, 27 Feb 2024)
EllapsedTime: 890.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TCGAbiolinks.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings TCGAbiolinks_2.31.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/TCGAbiolinks.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.31.3’
* 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  6.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    R      1.6Mb
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* 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
colDataPrepare: no visible binding for global variable
  ‘sample_submitter_id’
colDataPrepare: no visible binding for global variable ‘submitter_id’
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’
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’
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’
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’
Undefined global functions or variables:
  across assay.list barcode bcr_patient_barcode clinical coordinates
  days_to_last_followup everything exon geFDR2 gene_name is_ffpe logFC
  meFDR2 Read10X rse_gene sample_submitter_id starburst.status
  submitter_id threshold.starburst Tumor.purity 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
getManifest          10.354  1.358  89.274
TCGAanalyze_DEA       9.839  0.776  10.616
TCGAanalyze_LevelTab  5.042  0.160   5.202
GDCprepare_clinic     2.041  0.433  28.324
matchedMetExp         1.709  0.304  11.382
GDCquery              1.172  0.176   9.285
GDCquery_clinic       1.092  0.109   5.169
getResults            1.022  0.136   7.861
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.



Installation output

TCGAbiolinks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL TCGAbiolinks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 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 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 
 41.180   1.467  42.639 

Example timings

TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings

nameusersystemelapsed
GDCdownload0.0010.0000.001
GDCprepare000
GDCprepare_clinic 2.041 0.43328.324
GDCquery1.1720.1769.285
GDCquery_ATAC_seq0.4670.0650.985
GDCquery_clinic1.0920.1095.169
PanCancerAtlas_subtypes0.0160.0040.019
TCGAVisualize_volcano0.3440.0360.380
TCGA_MolecularSubtype0.2910.0240.315
TCGAanalyze_DEA 9.839 0.77610.616
TCGAanalyze_DEA_Affy0.0000.0000.001
TCGAanalyze_DMC0.9650.0991.064
TCGAanalyze_EA0.0010.0000.000
TCGAanalyze_EAcomplete2.3140.0962.409
TCGAanalyze_Filtering4.2110.2314.443
TCGAanalyze_LevelTab5.0420.1605.202
TCGAanalyze_Normalization1.3870.0401.427
TCGAanalyze_Pathview000
TCGAanalyze_Stemness1.5480.0401.588
TCGAanalyze_SurvivalKM0.1200.0120.132
TCGAanalyze_survival2.3600.0682.428
TCGAprepare_Affy000
TCGAquery_MatchedCoupledSampleTypes0.0020.0000.002
TCGAquery_SampleTypes0.0010.0000.001
TCGAquery_recount2000
TCGAquery_subtype0.0070.0000.007
TCGAtumor_purity0.060.000.06
TCGAvisualize_EAbarplot2.1020.0562.158
TCGAvisualize_Heatmap1.8640.0561.920
TCGAvisualize_PCA1.7560.0361.792
TCGAvisualize_meanMethylation2.6800.0512.731
TCGAvisualize_oncoprint0.0010.0000.000
TCGAvisualize_starburst0.0010.0000.000
UseRaw_afterFilter0.0010.0000.000
colDataPrepare0.2460.0000.899
dmc.non.parametric0.1320.0480.180
dmc.non.parametric.se0.1450.0200.165
gaiaCNVplot0.0280.0040.031
getAdjacencyBiogrid0.0010.0000.002
getDataCategorySummary1.0430.0842.862
getGDCInfo0.0730.0000.187
getGDCprojects0.0990.0000.251
getLinkedOmicsData0.0010.0000.000
getMC3MAF0.0000.0000.001
getManifest10.354 1.35889.274
getNbCases000
getNbFiles000
getProjectSummary0.1540.0200.444
getResults1.0220.1367.861
getSampleFilesSummary0.5850.1522.907
getTSS000
gliomaClassifier000
isServeOK0.0690.0000.186
matchedMetExp 1.709 0.30411.382