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This page was generated on 2023-10-16 11:36:44 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 2076/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.28.4  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/TCGAbiolinks
git_branch: RELEASE_3_17
git_last_commit: 40ea78f4
git_last_commit_date: 2023-10-05 12:52:55 -0400 (Thu, 05 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for TCGAbiolinks on palomino3


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: 2.28.4
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAbiolinks.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.28.4.tar.gz
StartedAt: 2023-10-16 07:33:33 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 07:41:42 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 488.7 seconds
RetCode: 0
Status:   OK  
CheckDir: TCGAbiolinks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAbiolinks.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.28.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/TCGAbiolinks.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TCGAbiolinks/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCGAbiolinks' version '2.28.4'
* 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 whether package 'TCGAbiolinks' can be installed ... OK
* checking installed package size ... NOTE
  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 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* 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 : <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_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'
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 assay.list barcode bcr_patient_barcode
  clinical coordinates days_to_last_followup everything exon geFDR2
  gene_name is_ffpe logFC meFDR2 rse_gene sample_submitter_id
  starburst.status submitter_id threshold.starburst 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
TCGAanalyze_DEA      11.30   0.33   11.62
getManifest           8.84   0.14   88.56
TCGAanalyze_LevelTab  6.06   0.14    6.21
GDCprepare_clinic     0.92   0.20   28.59
matchedMetExp         0.92   0.01    8.41
GDCquery              0.66   0.09    6.37
getResults            0.61   0.03    5.79
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/TCGAbiolinks.Rcheck/00check.log'
for details.



Installation output

TCGAbiolinks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL TCGAbiolinks
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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"
[ 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 
  50.40    2.54   53.00 

Example timings

TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings

nameusersystemelapsed
GDCdownload000
GDCprepare000
GDCprepare_clinic 0.92 0.2028.59
GDCquery0.660.096.37
GDCquery_ATAC_seq0.340.070.85
GDCquery_clinic0.800.003.05
PanCancerAtlas_subtypes0.080.000.07
TCGAVisualize_volcano0.450.030.61
TCGA_MolecularSubtype0.310.000.32
TCGAanalyze_DEA11.30 0.3311.62
TCGAanalyze_DEA_Affy000
TCGAanalyze_DMC1.000.041.05
TCGAanalyze_EA000
TCGAanalyze_EAcomplete2.500.192.68
TCGAanalyze_Filtering3.080.033.11
TCGAanalyze_LevelTab6.060.146.21
TCGAanalyze_Normalization1.300.071.36
TCGAanalyze_Pathview000
TCGAanalyze_Stemness1.420.031.45
TCGAanalyze_SurvivalKM0.120.010.14
TCGAanalyze_survival2.750.132.98
TCGAprepare_Affy000
TCGAquery_MatchedCoupledSampleTypes000
TCGAquery_SampleTypes000
TCGAquery_recount2000
TCGAquery_subtype000
TCGAtumor_purity0.080.000.08
TCGAvisualize_EAbarplot2.360.052.40
TCGAvisualize_Heatmap2.270.671.93
TCGAvisualize_PCA1.510.051.56
TCGAvisualize_meanMethylation2.780.052.83
TCGAvisualize_oncoprint000
TCGAvisualize_starburst000
UseRaw_afterFilter000
colDataPrepare0.080.000.52
dmc.non.parametric0.120.010.14
dmc.non.parametric.se0.190.000.19
gaiaCNVplot0.010.000.01
getAdjacencyBiogrid000
getDataCategorySummary1.000.022.61
getGDCInfo0.000.000.11
getGDCprojects0.050.000.14
getLinkedOmicsData000
getMC3MAF000
getManifest 8.84 0.1488.56
getNbCases000
getNbFiles000
getProjectSummary0.020.000.23
getResults0.610.035.79
getSampleFilesSummary0.390.001.20
getTSS000
gliomaClassifier000
isServeOK0.000.000.12
matchedMetExp0.920.018.41