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BioC 3.5: BUILD report for psygenet2r on oaxaca

This page was generated on 2017-03-04 16:51:53 -0500 (Sat, 04 Mar 2017).

Package 991/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psygenet2r 1.7.2
Alba Gutierrez-Sacristan
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/psygenet2r
Last Changed Rev: 126641 / Revision: 127142
Last Changed Date: 2017-02-09 11:27:43 -0500 (Thu, 09 Feb 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  ERROR  skipped  skipped 
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded [ ERROR ] skipped  skipped 

Summary

Package: psygenet2r
Version: 1.7.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data psygenet2r
StartedAt: 2017-03-03 20:46:12 -0800 (Fri, 03 Mar 2017)
EndedAt: 2017-03-03 20:49:43 -0800 (Fri, 03 Mar 2017)
EllapsedTime: 211.5 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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
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
Warning in psygenetGeneSentences(geneList = genesOfInterest, database = "ALL") :
  One or more of the given genes is not in PsyGeNET ( 'ALL' ). Genes: 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
Warning in singleInput.genes(diseases$diseases$`gene-list`$genes, psy, universe,  :
  Jaccard Index for all diseases in PsyGeNET will be calculated.

Error: processing vignette 'generalOverview.Rnw' failed with diagnostics:
 chunk 4 (label = dataGenet1) 
Error : `replacement` must be a character vector
Execution halted