############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data psygenet2r ### ############################################################################## ############################################################################## * 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