############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:geneLenDataBase.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings geneLenDataBase_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/geneLenDataBase.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘geneLenDataBase/DESCRIPTION’ ... OK * this is package ‘geneLenDataBase’ version ‘1.30.0’ * 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 ‘geneLenDataBase’ can be installed ... OK * checking installed package size ... NOTE installed size is 100.3Mb sub-directories of 1Mb or more: data 99.7Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 dependencies in R code ... NOTE ':::' call which should be '::': ‘GenomicFeatures:::supportedUCSCtables’ See the note in ?`:::` about the use of this operator. Unexported object imported by a ':::' call: ‘GenomicFeatures:::.UCSC_TXNAME2GENEID_MAPDEFS’ See the note in ?`:::` about the use of this operator. * 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'anoCar1.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'anoCar1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'anoCar1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'anoGam1.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'anoGam1.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'anoGam1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'apiMel1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'apiMel2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'apiMel2.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'apiMel2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'aplCal1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau2.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau2.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau3.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau3.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau3.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau3.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau3.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau3.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau4.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau4.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau4.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau4.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'bosTau4.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'braFlo1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'caeJap1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'caePb1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'caePb2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'caeRem2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'caeRem3.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'calJac1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'calJac1.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'calJac1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'canFam1.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'canFam1.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'canFam1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'canFam1.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'canFam1.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'canFam1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'canFam2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'canFam2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'canFam2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'canFam2.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'canFam2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'canFam2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'cavPor3.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'cavPor3.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'cavPor3.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'cavPor3.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'cb1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'cb3.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ce2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ce2.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ce2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ce4.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ce4.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ce4.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ce6.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ce6.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ce6.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ce6.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ci1.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ci1.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ci1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ci2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ci2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ci2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ci2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer3.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer3.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer3.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer4.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer4.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer4.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer4.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer4.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer5.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer5.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer5.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer5.vegaGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer5.vegaPseudoGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer6.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer6.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer6.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'danRer6.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dm1.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dm1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dm1.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dm2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dm2.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dm2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dm2.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dm2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dm3.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dm3.nscanPasaGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dm3.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dp2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dp2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dp3.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dp3.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'dp3.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droAna1.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droAna1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droAna1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droAna2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droAna2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droEre1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droEre1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droGri1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droGri1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droMoj1.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droMoj1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droMoj1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droMoj2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droMoj2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droPer1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droPer1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droSec1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droSec1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droSim1.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droSim1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droSim1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droVir1.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droVir1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droVir1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droVir2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droVir2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droYak1.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droYak1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droYak1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droYak2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'droYak2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'equCab1.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'equCab1.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'equCab1.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'equCab1.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'equCab1.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'equCab2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'equCab2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'equCab2.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'equCab2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'equCab2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'felCat3.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'felCat3.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'felCat3.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'felCat3.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'felCat3.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'felCat3.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'felCat3.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'felCat3.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'fr1.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'fr1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'fr2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'galGal2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'galGal2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'galGal2.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'galGal2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'galGal2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'galGal2.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'galGal3.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'galGal3.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'galGal3.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'galGal3.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'galGal3.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'galGal3.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'gasAcu1.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'gasAcu1.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg16.acembly.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg16.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg16.exoniphy.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg16.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg16.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg16.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg16.knownGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg16.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg16.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.acembly.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.acescan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.ccdsGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.exoniphy.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.knownGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.vegaGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.vegaPseudoGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg17.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.acembly.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.acescan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.ccdsGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.exoniphy.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.knownGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.knownGeneOld3.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.sibGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg18.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg19.ccdsGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg19.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg19.exoniphy.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg19.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg19.knownGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg19.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg19.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'hg19.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'loxAfr3.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm7.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm7.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm7.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm7.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm7.knownGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm7.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm7.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm7.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm8.ccdsGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm8.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm8.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm8.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm8.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm8.knownGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm8.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm8.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm8.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm8.sibGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm8.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm9.acembly.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm9.ccdsGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm9.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm9.exoniphy.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm9.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm9.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm9.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm9.knownGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm9.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm9.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm9.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'mm9.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom4.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom4.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom4.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom4.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom4.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom4.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom5.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom5.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom5.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom5.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom5.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'monDom5.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ornAna1.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ornAna1.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ornAna1.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ornAna1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'oryLat2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'oryLat2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'oryLat2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'oryLat2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'panTro1.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'panTro1.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'panTro1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'panTro1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'panTro2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'panTro2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'panTro2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'panTro2.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'panTro2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'panTro2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'petMar1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ponAbe2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ponAbe2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ponAbe2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ponAbe2.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ponAbe2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'ponAbe2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'priPac1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rheMac2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rheMac2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rheMac2.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rheMac2.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rheMac2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rheMac2.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rheMac2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn3.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn3.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn3.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn3.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn3.knownGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn3.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn3.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn3.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn3.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn4.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn4.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn4.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn4.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn4.knownGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn4.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn4.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn4.sgpGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'rn4.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'sacCer1.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'sacCer2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'strPur1.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'strPur1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'strPur1.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'strPur1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'strPur2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'strPur2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'strPur2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'strPur2.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'taeGut1.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'taeGut1.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'taeGut1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'taeGut1.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'taeGut1.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'taeGut1.xenoRefGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'tetNig1.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'tetNig1.geneid.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'tetNig1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'tetNig1.nscanGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'tetNig2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'xenTro1.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'xenTro2.ensGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'xenTro2.geneSymbol.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'xenTro2.genscan.LENGTH.Rd': ‘downloadLengthFromUCSC’ Missing link or links in documentation object 'xenTro2.refGene.LENGTH.Rd': ‘downloadLengthFromUCSC’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.14-data-experiment/meat/geneLenDataBase.Rcheck/00check.log’ for details.