Back to Workflows build report for BioC 3.15

This page was generated on 2022-10-18 14:00:09 -0400 (Tue, 18 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

BUILD results for SingscoreAMLMutations on merida1


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

raw results

Package 27/29HostnameOS / ArchINSTALLBUILD
SingscoreAMLMutations 1.12.0  (landing page)
Dharmesh D. Bhuva
Snapshot Date: 2022-10-18 07:45:02 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/SingscoreAMLMutations
git_branch: RELEASE_3_15
git_last_commit: 41e8654
git_last_commit_date: 2022-04-26 12:41:22 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  

Summary

Package: SingscoreAMLMutations
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SingscoreAMLMutations
StartedAt: 2022-10-18 08:12:59 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 08:14:25 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 86.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SingscoreAMLMutations
###
##############################################################################
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* checking for file ‘SingscoreAMLMutations/DESCRIPTION’ ... OK
* preparing ‘SingscoreAMLMutations’:
* checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
 OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘workflow_transcriptional_mut_sig.Rmd’ using rmarkdown
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-LAML
--------------------
oo Filtering results
--------------------
ooo By data.type
Quitting from lines 162-176 (workflow_transcriptional_mut_sig.Rmd) 
Error: processing vignette 'workflow_transcriptional_mut_sig.Rmd' failed with diagnostics:
Please set a valid workflow.type argument from the list below:
  => STAR - Counts
--- failed re-building ‘workflow_transcriptional_mut_sig.Rmd’

--- re-building ‘workflow_transcriptional_mut_sig_chinese.Rmd’ using rmarkdown
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-LAML
--------------------
oo Filtering results
--------------------
ooo By data.type
Quitting from lines 159-173 (workflow_transcriptional_mut_sig_chinese.Rmd) 
Error: processing vignette 'workflow_transcriptional_mut_sig_chinese.Rmd' failed with diagnostics:
Please set a valid workflow.type argument from the list below:
  => STAR - Counts
--- failed re-building ‘workflow_transcriptional_mut_sig_chinese.Rmd’

SUMMARY: processing the following files failed:
  ‘workflow_transcriptional_mut_sig.Rmd’
  ‘workflow_transcriptional_mut_sig_chinese.Rmd’

Error: Vignette re-building failed.
Execution halted