############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:synaptome.db.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings synaptome.db_0.99.16.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-data-annotation/meat/synaptome.db.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘synaptome.db/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘synaptome.db’ version ‘0.99.16’ * 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 ‘synaptome.db’ can be installed ... OK * checking installed package size ... OK * 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 code 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use loading from cache It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘BioNAR’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) findGeneByCompartmentPaperCnt.Rd:28: Lost braces; missing escapes or markup? 28 | Other {Gene functions}: | ^ checkRd: (-1) findGeneByPaperCnt.Rd:28: Lost braces; missing escapes or markup? 28 | Other {Gene functions}: | ^ checkRd: (-1) findGeneByPapers.Rd:33: Lost braces; missing escapes or markup? 33 | Other {Gene functions}: | ^ checkRd: (-1) findGenesByEntrez.Rd:36: Lost braces; missing escapes or markup? 36 | Other {Lookup functions}: | ^ checkRd: (-1) findGenesByEntrez.Rd:39: Lost braces; missing escapes or markup? 39 | Other {Gene functions}: | ^ checkRd: (-1) findGenesByName.Rd:34: Lost braces; missing escapes or markup? 34 | Other {Lookup functions}: | ^ checkRd: (-1) findGenesByName.Rd:37: Lost braces; missing escapes or markup? 37 | Other {Gene functions}: | ^ checkRd: (-1) getAllGenes4BrainRegion.Rd:44: Lost braces; missing escapes or markup? 44 | Other {BrainRegion functions}: | ^ checkRd: (-1) getAllGenes4BrainRegion.Rd:49: Lost braces; missing escapes or markup? 49 | Other {BrainRegion Gene functions}: | ^ checkRd: (-1) getAllGenes4Compartment.Rd:25: Lost braces; missing escapes or markup? 25 | Other {Gene functions}: | ^ checkRd: (-1) getAllGenes4Compartment.Rd:34: Lost braces; missing escapes or markup? 34 | Other {Compartment functions}: | ^ checkRd: (-1) getBrainRegions.Rd:27: Lost braces; missing escapes or markup? 27 | Other {BrainRegion functions}: | ^ checkRd: (-1) getCompartments.Rd:21: Lost braces; missing escapes or markup? 21 | Other {Compartment functions}: | ^ checkRd: (-1) getGeneDiseaseByEntres.Rd:30: Lost braces; missing escapes or markup? 30 | Other {Disease functions}: | ^ checkRd: (-1) getGeneDiseaseByIDs.Rd:30: Lost braces; missing escapes or markup? 30 | Other {Disease functions}: | ^ checkRd: (-1) getGeneDiseaseByName.Rd:24: Lost braces; missing escapes or markup? 24 | Other {Disease functions}: | ^ checkRd: (-1) getGeneInfoByEntrez.Rd:39: Lost braces; missing escapes or markup? 39 | Other {GeneInfo functions}: | ^ checkRd: (-1) getGeneInfoByIDs.Rd:50: Lost braces; missing escapes or markup? 50 | Other {GeneInfo functions}: | ^ checkRd: (-1) getGeneInfoByName.Rd:54: Lost braces; missing escapes or markup? 54 | Other {GeneInfo functions}: | ^ checkRd: (-1) getGeneInfoByPapers.Rd:58: Lost braces; missing escapes or markup? 58 | Other {GeneInfo functions}: | ^ checkRd: (-1) getGenes4BrainRegion.Rd:49: Lost braces; missing escapes or markup? 49 | Other {BrainRegion functions}: | ^ checkRd: (-1) getGenes4BrainRegion.Rd:54: Lost braces; missing escapes or markup? 54 | Other {BrainRegion Gene functions}: | ^ checkRd: (-1) getGenes4Compartment.Rd:34: Lost braces; missing escapes or markup? 34 | Other {Gene functions}: | ^ checkRd: (-1) getGenes4Compartment.Rd:43: Lost braces; missing escapes or markup? 43 | Other {Compartment functions}: | ^ checkRd: (-1) getGenesByID.Rd:33: Lost braces; missing escapes or markup? 33 | Other {Gene functions}: | ^ checkRd: (-1) getIGraphFromPPI.Rd:40: Lost braces; missing escapes or markup? 40 | Other {PPI functions}: | ^ checkRd: (-1) getMutations4DiseaseByEntres.Rd:31: Lost braces; missing escapes or markup? 31 | Other {Mutation functions}: | ^ checkRd: (-1) getMutations4DiseaseByIDs.Rd:54: Lost braces; missing escapes or markup? 54 | Other {Mutation functions}: | ^ checkRd: (-1) getMutations4DiseaseByName.Rd:33: Lost braces; missing escapes or markup? 33 | Other {Mutation functions}: | ^ checkRd: (-1) getPPIbyEntrez.Rd:42: Lost braces; missing escapes or markup? 42 | Other {PPI functions}: | ^ checkRd: (-1) getPPIbyIDs.Rd:42: Lost braces; missing escapes or markup? 42 | Other {PPI functions}: | ^ checkRd: (-1) getPPIbyIDs4BrainRegion.Rd:56: Lost braces; missing escapes or markup? 56 | Other {PPI functions}: | ^ checkRd: (-1) getPPIbyIDs4BrainRegion.Rd:64: Lost braces; missing escapes or markup? 64 | Other {BrainRegion functions}: | ^ checkRd: (-1) getPPIbyIDs4Compartment.Rd:39: Lost braces; missing escapes or markup? 39 | Other {PPI functions}: | ^ checkRd: (-1) getPPIbyIDs4Compartment.Rd:47: Lost braces; missing escapes or markup? 47 | Other {Compartment functions}: | ^ checkRd: (-1) getPPIbyName.Rd:44: Lost braces; missing escapes or markup? 44 | Other {PPI functions}: | ^ checkRd: (-1) getTableFromPPI.Rd:44: Lost braces; missing escapes or markup? 44 | Other {PPI functions}: | ^ * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.19-data-annotation/meat/synaptome.db.Rcheck/00check.log’ for details.