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This page was generated on 2023-01-02 09:00:53 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for TCGAbiolinks on palomino5


To the developers/maintainers of the TCGAbiolinks package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2008/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.27.0  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/TCGAbiolinks
git_branch: master
git_last_commit: 15acadb
git_last_commit_date: 2022-11-01 11:12:02 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  

Summary

Package: TCGAbiolinks
Version: 2.27.0
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_2.27.0.tar.gz
StartedAt: 2022-12-29 04:07:44 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 04:24:36 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 1011.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: TCGAbiolinks.Rcheck
Warnings: NA

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_2.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAbiolinks.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '2.27.0'
* 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 dependencies in R code ... WARNING
'library' or 'require' call not declared from: 'dplyr'
'library' or 'require' calls in package code:
  'dplyr' 'maftools'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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'
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'
colDataPrepare: no visible binding for global variable 'sample_type'
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'
readSingleCellAnalysis : <anonymous>: no visible global function
  definition for 'Read10X'
Undefined global functions or variables:
  Read10X Tumor.purity assay.list barcode bcr_patient_barcode clinical
  coordinates days_to_last_followup exon geFDR2 gene_name is_ffpe logFC
  meFDR2 rse_gene sample_submitter_id sample_type 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 ... ERROR
Running examples in 'TCGAbiolinks-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TCGAvisualize_meanMethylation
> ### Title: Mean methylation boxplot
> ### Aliases: TCGAvisualize_meanMethylation
> 
> ### ** Examples
> 
> nrows <- 200; ncols <- 21
> counts <- matrix(runif(nrows * ncols, 0, 1), nrows)
> rowRanges <- GenomicRanges::GRanges(rep(c("chr1", "chr2"), c(50, 150)),
+                    IRanges::IRanges(floor(runif(200, 1e5, 1e6)), width=100),
+                     strand=sample(c("+", "-"), 200, TRUE),
+                     feature_id=sprintf("ID%03d", 1:200))
> colData <- S4Vectors::DataFrame(Treatment=rep(c("ChIP", "Input","Other"), 7),
+                     row.names=LETTERS[1:21],
+                     group=rep(c("group1","group2","group3"),c(7,7,7)),
+                     subgroup=rep(c("subgroup1","subgroup2","subgroup3"),7))
> data <- SummarizedExperiment::SummarizedExperiment(
+          assays=S4Vectors::SimpleList(counts=counts),
+          rowRanges=rowRanges,
+          colData=colData)
> TCGAvisualize_meanMethylation(data,groupCol  = "group")
==================== DATA Summary ====================
  groups      Mean    Median       Max       Min
1 group1 0.4935503 0.4844465 0.5193171 0.4690160
2 group2 0.4913444 0.4878388 0.5334364 0.4502542
3 group3 0.4970774 0.5012800 0.5218784 0.4649520
==================== END DATA Summary ====================
==================== T test results ====================
          group1    group2    group3
group1        NA 0.8649153 0.7425559
group2 0.8649153        NA 0.6447791
group3 0.7425559 0.6447791        NA
==================== END T test results ====================
 [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2"
 [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3"
[17] "group3" "group3" "group3" "group3" "group3"
 [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2"
 [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3"
[17] "group3" "group3" "group3" "group3" "group3"
[1] "#FF0000" "#00FF00" "#0000FF"
Plot saved in:  F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAbiolinks.Rcheck/groupMeanMet.pdf
> # change lower/upper y-axis limit
> TCGAvisualize_meanMethylation(data,groupCol  = "group", y.limits = c(0,1))
==================== DATA Summary ====================
  groups      Mean    Median       Max       Min
1 group1 0.4935503 0.4844465 0.5193171 0.4690160
2 group2 0.4913444 0.4878388 0.5334364 0.4502542
3 group3 0.4970774 0.5012800 0.5218784 0.4649520
==================== END DATA Summary ====================
==================== T test results ====================
          group1    group2    group3
group1        NA 0.8649153 0.7425559
group2 0.8649153        NA 0.6447791
group3 0.7425559 0.6447791        NA
==================== END T test results ====================
 [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2"
 [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3"
[17] "group3" "group3" "group3" "group3" "group3"
 [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2"
 [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3"
[17] "group3" "group3" "group3" "group3" "group3"
[1] "#FF0000" "#00FF00" "#0000FF"
Plot saved in:  F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAbiolinks.Rcheck/groupMeanMet.pdf
> # change lower y-axis limit
> TCGAvisualize_meanMethylation(data,groupCol  = "group", y.limits = 0)
==================== DATA Summary ====================
  groups      Mean    Median       Max       Min
1 group1 0.4935503 0.4844465 0.5193171 0.4690160
2 group2 0.4913444 0.4878388 0.5334364 0.4502542
3 group3 0.4970774 0.5012800 0.5218784 0.4649520
==================== END DATA Summary ====================
==================== T test results ====================
          group1    group2    group3
group1        NA 0.8649153 0.7425559
group2 0.8649153        NA 0.6447791
group3 0.7425559 0.6447791        NA
==================== END T test results ====================
 [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2"
 [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3"
[17] "group3" "group3" "group3" "group3" "group3"
 [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2"
 [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3"
[17] "group3" "group3" "group3" "group3" "group3"
[1] "#FF0000" "#00FF00" "#0000FF"
Plot saved in:  F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAbiolinks.Rcheck/groupMeanMet.pdf
> TCGAvisualize_meanMethylation(data,groupCol  = "group", subgroupCol="subgroup")
==================== DATA Summary ====================
  groups      Mean    Median       Max       Min
1 group1 0.4935503 0.4844465 0.5193171 0.4690160
2 group2 0.4913444 0.4878388 0.5334364 0.4502542
3 group3 0.4970774 0.5012800 0.5218784 0.4649520
==================== END DATA Summary ====================
==================== T test results ====================
          group1    group2    group3
group1        NA 0.8649153 0.7425559
group2 0.8649153        NA 0.6447791
group3 0.7425559 0.6447791        NA
==================== END T test results ====================
 [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2"
 [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3"
[17] "group3" "group3" "group3" "group3" "group3"
 [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2"
 [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3"
[17] "group3" "group3" "group3" "group3" "group3"
[1] "#FF0000" "#00FF00" "#0000FF"
Plot saved in:  F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAbiolinks.Rcheck/groupMeanMet.pdf
> TCGAvisualize_meanMethylation(data,groupCol  = "group")
==================== DATA Summary ====================
  groups      Mean    Median       Max       Min
1 group1 0.4935503 0.4844465 0.5193171 0.4690160
2 group2 0.4913444 0.4878388 0.5334364 0.4502542
3 group3 0.4970774 0.5012800 0.5218784 0.4649520
==================== END DATA Summary ====================
==================== T test results ====================
          group1    group2    group3
group1        NA 0.8649153 0.7425559
group2 0.8649153        NA 0.6447791
group3 0.7425559 0.6447791        NA
==================== END T test results ====================
 [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2"
 [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3"
[17] "group3" "group3" "group3" "group3" "group3"
 [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2"
 [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3"
[17] "group3" "group3" "group3" "group3" "group3"
[1] "#FF0000" "#00FF00" "#0000FF"
Error in grDevices::pdf(file = filename, ..., version = version) : 
  cannot open file 'groupMeanMet.pdf'
Calls: TCGAvisualize_meanMethylation -> ggsave -> dev -> <Anonymous>
Execution halted
* 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 ERROR, 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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 6 | SKIP 22 | PASS 45 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (22)

[ FAIL 0 | WARN 6 | SKIP 22 | PASS 45 ]
> 
> proc.time()
   user  system elapsed 
  97.26    3.00  105.54

Example timings

TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings

nameusersystemelapsed
GDCdownload 2.60 0.1433.23
GDCprepare000
GDCprepare_clinic 1.82 0.1153.08
GDCquery0.470.015.22
GDCquery_ATAC_seq0.270.050.70
GDCquery_clinic550.30 16.06585.86
PanCancerAtlas_subtypes0.010.000.03
TCGAVisualize_volcano0.490.020.58
TCGA_MolecularSubtype0.250.000.25
TCGAanalyze_DEA8.340.238.61
TCGAanalyze_DEA_Affy000
TCGAanalyze_DMC0.700.030.73
TCGAanalyze_EA000
TCGAanalyze_EAcomplete1.990.032.02
TCGAanalyze_Filtering3.220.043.25
TCGAanalyze_LevelTab5.000.035.03
TCGAanalyze_Normalization1.090.001.09
TCGAanalyze_Pathview000
TCGAanalyze_Stemness1.30.01.3
TCGAanalyze_SurvivalKM0.110.000.11
TCGAanalyze_survival2.120.062.25
TCGAprepare_Affy000
TCGAquery_MatchedCoupledSampleTypes000
TCGAquery_SampleTypes000
TCGAquery_recount2000
TCGAquery_subtype0.020.000.01
TCGAtumor_purity0.060.000.07
TCGAvisualize_EAbarplot2.010.002.01
TCGAvisualize_Heatmap1.540.001.53
TCGAvisualize_PCA2.170.032.21