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This page was generated on 2024-04-15 11:32:22 -0400 (Mon, 15 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 2112/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.30.4  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2024-04-13 09:00:03 -0400 (Sat, 13 Apr 2024)
git_url: https://git.bioconductor.org/packages/TCGAbiolinks
git_branch: RELEASE_3_18
git_last_commit: 6a9b2571
git_last_commit_date: 2024-03-26 11:41:22 -0400 (Tue, 26 Mar 2024)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for TCGAbiolinks on kjohnson1


To the developers/maintainers of the TCGAbiolinks package:
- 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: 2.30.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TCGAbiolinks_2.30.4.tar.gz
StartedAt: 2024-04-15 05:18:27 -0400 (Mon, 15 Apr 2024)
EndedAt: 2024-04-15 05:30:40 -0400 (Mon, 15 Apr 2024)
EllapsedTime: 732.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: TCGAbiolinks.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TCGAbiolinks_2.30.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/TCGAbiolinks.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.30.4’
* 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 for sufficient/correct file permissions ... 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 ... 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 : <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 ... ERROR
Running examples in ‘TCGAbiolinks-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getManifest
> ### Title: Get a Manifest from GDCquery output that can be used with
> ###   GDC-client
> ### Aliases: getManifest
> 
> ### ** Examples
> 
> query <- GDCquery(
+   project = "TARGET-AML",
+   data.category = "Transcriptome Profiling",
+   data.type = "Gene Expression Quantification",
+   workflow.type = "STAR - Counts",
+   barcode = c("TARGET-20-PADZCG-04A-01R", "TARGET-20-PARJCR-09A-01R")
+ )
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TARGET-AML
Warning in open.connection(con, "rb") :
  cannot open URL 'https://api.gdc.cancer.gov/files/?pretty=true&expand=cases,cases.samples.portions.analytes.aliquots,cases.project,center,analysis,cases.samples&size=10246&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TARGET-AML%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22STAR%20-%20Counts%22]%7D%7D]%7D&format=JSON': HTTP status was '504 Gateway Timeout'
Warning in open.connection(con, "rb") :
  cannot open URL 'https://api.gdc.cancer.gov/files/?pretty=true&expand=cases,cases.samples.portions.analytes.aliquots,cases.project,center,analysis,cases.samples&size=10246&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TARGET-AML%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22STAR%20-%20Counts%22]%7D%7D]%7D&format=JSON': HTTP status was '504 Gateway Timeout'
Warning in open.connection(con, "rb") :
  cannot open URL 'https://api.gdc.cancer.gov/files/?pretty=true&expand=cases,cases.samples.portions.analytes.aliquots,cases.project,center,analysis,cases.samples&size=10246&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TARGET-AML%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22STAR%20-%20Counts%22]%7D%7D]%7D&format=JSON': HTTP status was '504 Gateway Timeout'
Error:  Error in getURL(url, fromJSON, timeout(600), simplifyDataFrame = TRUE): 'getURL()' failed:
  URL: https://api.gdc.cancer.gov/files/?pretty=true&expand=cases,cases.samples.portions.analytes.aliquots,cases.project,center,analysis,cases.samples&size=10246&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TARGET-AML%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22STAR%20-%20Counts%22]%7D%7D]%7D&format=JSON
  error: cannot open the connection to 'https://api.gdc.cancer.gov/files/?pretty=true&expand=cases,cases.samples.portions.analytes.aliquots,cases.project,center,analysis,cases.samples&size=10246&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TARGET-AML%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22STAR%20-%20Counts%22]%7D%7D]%7D&format=JSON'

We will retry to access GDC!
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE HTML PUBLIC "-//IETF/
                     (right here) ------^
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test-analyse.R:153:9'): Results of TCGAanalyze_DEA inverting groups changes signal and order of the signals are right ──
  dataDEGs$logFC not equal to -1 * dataDEGs.inv$logFC.
  8/15396 mismatches (average diff: 0.852)
  [7378]   0.638 - -0.634 ==  1.272
  [7379]  -0.634 -  0.638 == -1.272
  [9519]  -0.429 -  0.429 == -0.858
  [9520]   0.429 - -0.429 ==  0.858
  [10555]  0.365 - -0.355 ==  0.720
  [10556] -0.355 -  0.365 == -0.720
  [11525]  0.279 - -0.279 ==  0.558
  [11526] -0.279 -  0.279 == -0.558
  
  [ FAIL 1 | WARN 0 | SKIP 24 | PASS 31 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/TCGAbiolinks.Rcheck/00check.log’
for details.

Installation output

TCGAbiolinks.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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.fail


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 1 | 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'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-analyse.R:153:9'): Results of TCGAanalyze_DEA inverting groups changes signal and order of the signals are right ──
dataDEGs$logFC not equal to -1 * dataDEGs.inv$logFC.
8/15396 mismatches (average diff: 0.852)
[7378]   0.638 - -0.634 ==  1.272
[7379]  -0.634 -  0.638 == -1.272
[9519]  -0.429 -  0.429 == -0.858
[9520]   0.429 - -0.429 ==  0.858
[10555]  0.365 - -0.355 ==  0.720
[10556] -0.355 -  0.365 == -0.720
[11525]  0.279 - -0.279 ==  0.558
[11526] -0.279 -  0.279 == -0.558

[ FAIL 1 | WARN 0 | SKIP 24 | PASS 31 ]
Error: Test failures
Execution halted

Example timings

TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings

nameusersystemelapsed
GDCdownload0.0000.0010.001
GDCprepare0.0000.0010.001
GDCprepare_clinic 0.930 0.13338.370
GDCquery 0.850 0.07412.821
GDCquery_ATAC_seq1.2110.0454.034
GDCquery_clinic0.6480.0427.216
PanCancerAtlas_subtypes0.0130.0020.016
TCGAVisualize_volcano0.3010.0200.338
TCGA_MolecularSubtype0.1750.0040.181
TCGAanalyze_DEA13.413 0.42313.975
TCGAanalyze_DEA_Affy000
TCGAanalyze_DMC1.0040.0781.087
TCGAanalyze_EA0.0000.0010.000
TCGAanalyze_EAcomplete2.4130.0932.534
TCGAanalyze_Filtering4.8280.1205.006
TCGAanalyze_LevelTab6.7460.2127.088
TCGAanalyze_Normalization3.6410.0573.739
TCGAanalyze_Pathview0.0010.0000.000
TCGAanalyze_Stemness2.0180.0642.091
TCGAanalyze_SurvivalKM0.1460.0090.161
TCGAanalyze_survival2.6320.0812.770
TCGAprepare_Affy000
TCGAquery_MatchedCoupledSampleTypes0.0020.0000.002
TCGAquery_SampleTypes0.0000.0010.001
TCGAquery_recount20.0000.0000.001
TCGAquery_subtype0.0110.0010.011
TCGAtumor_purity0.0750.0010.075
TCGAvisualize_EAbarplot2.3210.0672.398
TCGAvisualize_Heatmap2.0930.0782.186
TCGAvisualize_PCA2.0160.0572.088
TCGAvisualize_meanMethylation2.8340.0572.917
TCGAvisualize_oncoprint0.0000.0010.001
TCGAvisualize_starburst0.0000.0000.001
UseRaw_afterFilter0.0000.0000.001
colDataPrepare0.1390.0071.740
dmc.non.parametric0.0850.0140.104
dmc.non.parametric.se0.1460.0100.157
gaiaCNVplot0.0330.0020.035
getAdjacencyBiogrid0.0020.0000.002
getDataCategorySummary1.0450.0234.521
getGDCInfo0.0270.0020.498
getGDCprojects0.0190.0010.359
getLinkedOmicsData000
getMC3MAF000