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This page was generated on 2022-07-07 11:11:46 -0400 (Thu, 07 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4160
kjohnsonmacOS 12.4 Montereyarm644.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" 3115
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 psygenet2r on kjohnson


To the developers/maintainers of the psygenet2r package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/psygenet2r.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1507/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psygenet2r 1.29.0  (landing page)
Alba Gutierrez-Sacristan
Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022)
git_url: https://git.bioconductor.org/packages/psygenet2r
git_branch: master
git_last_commit: 253c4b6
git_last_commit_date: 2022-04-26 11:29:58 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.2.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnsonmacOS 12.4 Monterey / arm64  OK    ERROR  skippedskipped

Summary

Package: psygenet2r
Version: 1.29.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data psygenet2r
StartedAt: 2022-07-07 02:37:35 -0400 (Thu, 07 Jul 2022)
EndedAt: 2022-07-07 02:49:29 -0400 (Thu, 07 Jul 2022)
EllapsedTime: 714.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data psygenet2r
###
##############################################################################
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* checking for file ‘psygenet2r/DESCRIPTION’ ... OK
* preparing ‘psygenet2r’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘case_study.Rmd’ using rmarkdown
Warning in psygenetGene(geneList, database, verbose = verbose) :
  One or more of the given genes is not in PsyGeNET ( 'ALL' ):
AKAP13, ANKS1A, ATP6V1G3, C11orf80, CACNB3, CROT, DNAJB4, DUSP22, FAM155A, FLJ16124, FSTL5, GATA5, GNA14, GPR81, IFI44, KDM5B, KIF1A, LOC150197, MAPK10, MCM9, MSI2, ODZ4, PAPOLG, PAX1, PTPRE, PTPRT, RASIP1, RIMBP2, RXRG, SGCG, SIPA1L2, SNX8, SPERT, STK39, THSD7A, TNR, TRANK1, TRIM9, UBE2E3, UBR1, ZMIZ1, ZNF274
Quitting from lines 191-196 (case_study.Rmd) 
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
argument 'x' must be a raw vector
--- failed re-building ‘case_study.Rmd’

--- re-building ‘general_overview.Rmd’ using rmarkdown
Warning: The `space` argument of `gradient_n_pal()` only supports be "Lab" as of scales 0.3.0.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Warning in singleInput.genes(diseases$diseases$geneList$genes, psy, universe,  :
  Jaccard Index for all diseases in PsyGeNET will be calculated.
--- finished re-building ‘general_overview.Rmd’

SUMMARY: processing the following file failed:
  ‘case_study.Rmd’

Error: Vignette re-building failed.
Execution halted