Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2021-10-15 15:06:55 -0400 (Fri, 15 Oct 2021).

CHECK results for TCGAbiolinks on machv2

To the developers/maintainers of the TCGAbiolinks package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1899/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.20.1  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/TCGAbiolinks
git_branch: RELEASE_3_13
git_last_commit: d7830c91
git_last_commit_date: 2021-10-04 16:09:51 -0400 (Mon, 04 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: TCGAbiolinks
Version: 2.20.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TCGAbiolinks_2.20.1.tar.gz
StartedAt: 2021-10-15 00:37:07 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 00:47:27 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 619.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TCGAbiolinks.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TCGAbiolinks_2.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.20.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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  7.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    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 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 dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘sesameData’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GDCquery : <anonymous>: no visible binding for global variable
  ‘submitter_id’
GDCquery : <anonymous>: no visible binding for global variable
  ‘is_ffpe’
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 global function definition for
  ‘values’
readExonQuantification: no visible binding for global variable ‘exon’
readExonQuantification: no visible binding for global variable
  ‘coordinates’
readGeneExpressionQuantification : <anonymous>: no visible binding for
  '<<-' assignment to ‘assay.list’
readGeneExpressionQuantification: no visible binding for global
  variable ‘assay.list’
Undefined global functions or variables:
  Tumor.purity assay.list barcode clinical coordinates exon is_ffpe
  rse_gene submitter_id value values
* 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_LevelTab      18.665  2.134  20.810
GDCquery_clinic           19.552  0.336  37.488
TCGAanalyze_DEA           13.692  0.278  13.982
TCGAanalyze_Filtering     10.229  0.106  10.341
TCGAvisualize_PCA          6.080  0.082   6.167
TCGAanalyze_Stemness       5.274  0.046   5.327
TCGAanalyze_Normalization  4.988  0.038   5.029
GDCdownload                4.434  0.199  39.519
GDCprepare_clinic          3.050  0.137  51.248
getDataCategorySummary     1.978  0.029   5.344
GDCquery                   0.848  0.019   6.079
getManifest                0.831  0.011   7.134
getResults                 0.735  0.011   5.951
matchedMetExp              0.676  0.019   5.778
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.



Installation output

TCGAbiolinks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TCGAbiolinks
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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"
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (21)

[ FAIL 0 | WARN 4 | SKIP 21 | PASS 45 ]
> 
> proc.time()
   user  system elapsed 
 62.731   2.126  70.628 

Example timings

TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings

nameusersystemelapsed
GDCdownload 4.434 0.19939.519
GDCprepare0.0010.0010.001
GDCprepare_clinic 3.050 0.13751.248
GDCquery0.8480.0196.079
GDCquery_ATAC_seq0.5970.0251.397
GDCquery_Maf0.0000.0000.001
GDCquery_clinic19.552 0.33637.488
PanCancerAtlas_subtypes0.0220.0020.024
TCGAVisualize_volcano0.3570.0110.369
TCGA_MolecularSubtype0.5330.0030.535
TCGAanalyze_DEA13.692 0.27813.982
TCGAanalyze_DEA_Affy0.0000.0000.001
TCGAanalyze_DMC1.5420.0651.652
TCGAanalyze_EA0.0000.0010.001
TCGAanalyze_EAcomplete3.6290.0763.707
TCGAanalyze_Filtering10.229 0.10610.341
TCGAanalyze_LevelTab18.665 2.13420.810
TCGAanalyze_Normalization4.9880.0385.029
TCGAanalyze_Pathview0.0000.0000.001
TCGAanalyze_Stemness5.2740.0465.327
TCGAanalyze_SurvivalKM0.1780.0080.187
TCGAanalyze_survival3.8830.1494.040
TCGAprepare_Affy0.0000.0000.001
TCGAquery_MatchedCoupledSampleTypes0.0030.0000.004
TCGAquery_SampleTypes0.0020.0010.002
TCGAquery_recount2000
TCGAquery_subtype0.0090.0010.009
TCGAtumor_purity0.090.000.09
TCGAvisualize_EAbarplot3.7710.0873.862
TCGAvisualize_Heatmap3.0940.0623.160
TCGAvisualize_PCA6.0800.0826.167
TCGAvisualize_meanMethylation3.2880.0483.343
TCGAvisualize_oncoprint0.0000.0010.001
TCGAvisualize_starburst0.0000.0020.002
UseRaw_afterFilter0.0000.0010.001
colDataPrepare0.1870.0050.785
dmc.non.parametric0.1960.0400.237
dmc.non.parametric.se0.3260.0160.342
gaiaCNVplot0.0390.0020.041
getAdjacencyBiogrid0.0020.0010.003
getDataCategorySummary1.9780.0295.344
getGDCInfo0.0250.0020.246
getGDCprojects0.0380.0020.221
getLinkedOmicsData000
getMC3MAF000
getManifest0.8310.0117.134
getNbCases000
getNbFiles000
getProjectSummary000
getResults0.7350.0115.951
getSampleFilesSummary0.4470.0081.707
getTSS000
gliomaClassifier0.0000.0010.000
isServeOK0.0250.0020.251
matchedMetExp0.6760.0195.778