Back to Build/check report for BioC 3.19 experimental data
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This page was generated on 2024-05-16 14:51:31 -0400 (Thu, 16 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
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

Package 145/430HostnameOS / ArchINSTALLBUILDCHECK
geneLenDataBase 1.40.0  (landing page)
Matthew Young , Nadia Davidson
Snapshot Date: 2024-05-16 07:30:03 -0400 (Thu, 16 May 2024)
git_url: https://git.bioconductor.org/packages/geneLenDataBase
git_branch: RELEASE_3_19
git_last_commit: 95fca4d
git_last_commit_date: 2024-04-30 10:29:33 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  

CHECK results for geneLenDataBase on nebbiolo1


To the developers/maintainers of the geneLenDataBase package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: geneLenDataBase
Version: 1.40.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:geneLenDataBase.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings geneLenDataBase_1.40.0.tar.gz
StartedAt: 2024-05-16 11:26:09 -0400 (Thu, 16 May 2024)
EndedAt: 2024-05-16 11:34:51 -0400 (Thu, 16 May 2024)
EllapsedTime: 522.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: geneLenDataBase.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:geneLenDataBase.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings geneLenDataBase_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/geneLenDataBase.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 ‘geneLenDataBase/DESCRIPTION’ ... OK
* this is package ‘geneLenDataBase’ version ‘1.40.0’
* 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 100.0Mb
  sub-directories of 1Mb or more:
    data  99.5Mb
* 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 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 dependencies in R code ... NOTE
':::' call which should be '::': ‘GenomicFeatures:::supportedUCSCtables’
  See the note in ?`:::` about the use of this operator.
Missing object imported by a ':::' call: ‘GenomicFeatures:::.UCSC_TXNAME2GENEID_MAPDEFS’
* 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) unfactor.Rd:21: Lost braces
    21 | As factors are their own type, to remove factors we must convert each level into another type.  This is currently done using "typeless" behaviour: a factor is converted to a numeric vector if this can be done without inducing NAs, otherwise it is coerced using as.character. Currently supported types are: /code{factor}, /code{data.frame} and /code{list}.
       |                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) unfactor.Rd:21: Lost braces
    21 | As factors are their own type, to remove factors we must convert each level into another type.  This is currently done using "typeless" behaviour: a factor is converted to a numeric vector if this can be done without inducing NAs, otherwise it is coerced using as.character. Currently supported types are: /code{factor}, /code{data.frame} and /code{list}.
       |                                                                                                                                                                                                                                                                                                                                       ^
checkRd: (-1) unfactor.Rd:21: Lost braces
    21 | As factors are their own type, to remove factors we must convert each level into another type.  This is currently done using "typeless" behaviour: a factor is converted to a numeric vector if this can be done without inducing NAs, otherwise it is coerced using as.character. Currently supported types are: /code{factor}, /code{data.frame} and /code{list}.
       |                                                                                                                                                                                                                                                                                                                                                             ^
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'anoCar1.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'anoCar1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'anoCar1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'anoGam1.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'anoGam1.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'anoGam1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'apiMel1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'apiMel2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'apiMel2.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'apiMel2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'aplCal1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau2.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau2.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau2.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau3.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau3.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau3.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau3.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau3.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau3.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau4.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau4.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau4.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau4.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'bosTau4.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'braFlo1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'caeJap1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'caePb1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'caePb2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'caeRem2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'caeRem3.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'calJac1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'calJac1.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'calJac1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'canFam1.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'canFam1.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'canFam1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'canFam1.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'canFam1.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'canFam1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'canFam2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'canFam2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'canFam2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'canFam2.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'canFam2.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'canFam2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'cavPor3.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'cavPor3.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'cavPor3.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'cavPor3.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'cb1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'cb3.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ce2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ce2.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ce2.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ce4.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ce4.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ce4.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ce6.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ce6.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ce6.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ce6.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ci1.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ci1.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ci1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ci2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ci2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ci2.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ci2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer3.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer3.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer3.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer4.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer4.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer4.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer4.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer4.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer5.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer5.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer5.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer5.vegaGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer5.vegaPseudoGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer6.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer6.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer6.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'danRer6.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dm1.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dm1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dm1.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dm2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dm2.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dm2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dm2.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dm2.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dm3.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dm3.nscanPasaGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dm3.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dp2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dp2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dp3.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dp3.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'dp3.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droAna1.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droAna1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droAna1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droAna2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droAna2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droEre1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droEre1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droGri1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droGri1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droMoj1.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droMoj1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droMoj1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droMoj2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droMoj2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droPer1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droPer1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droSec1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droSec1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droSim1.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droSim1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droSim1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droVir1.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droVir1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droVir1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droVir2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droVir2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droYak1.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droYak1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droYak1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droYak2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'droYak2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'equCab1.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'equCab1.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'equCab1.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'equCab1.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'equCab1.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'equCab2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'equCab2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'equCab2.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'equCab2.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'equCab2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'felCat3.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'felCat3.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'felCat3.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'felCat3.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'felCat3.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'felCat3.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'felCat3.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'felCat3.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'fr1.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'fr1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'fr2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'galGal2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'galGal2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'galGal2.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'galGal2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'galGal2.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'galGal2.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'galGal3.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'galGal3.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'galGal3.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'galGal3.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'galGal3.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'galGal3.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'gasAcu1.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'gasAcu1.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg16.acembly.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg16.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg16.exoniphy.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg16.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg16.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg16.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg16.knownGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg16.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg16.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.acembly.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.acescan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.ccdsGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.exoniphy.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.knownGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.vegaGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.vegaPseudoGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg17.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.acembly.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.acescan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.ccdsGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.exoniphy.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.knownGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.knownGeneOld3.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.sibGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg18.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg19.ccdsGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg19.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg19.exoniphy.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg19.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg19.knownGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg19.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg19.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'hg19.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'loxAfr3.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm7.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm7.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm7.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm7.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm7.knownGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm7.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm7.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm7.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm8.ccdsGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm8.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm8.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm8.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm8.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm8.knownGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm8.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm8.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm8.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm8.sibGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm8.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm9.acembly.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm9.ccdsGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm9.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm9.exoniphy.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm9.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm9.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm9.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm9.knownGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm9.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm9.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm9.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'mm9.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom4.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom4.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom4.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom4.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom4.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom4.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom5.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom5.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom5.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom5.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom5.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'monDom5.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ornAna1.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ornAna1.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ornAna1.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ornAna1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'oryLat2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'oryLat2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'oryLat2.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'oryLat2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'panTro1.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'panTro1.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'panTro1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'panTro1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'panTro2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'panTro2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'panTro2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'panTro2.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'panTro2.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'panTro2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'petMar1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ponAbe2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ponAbe2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ponAbe2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ponAbe2.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ponAbe2.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'ponAbe2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'priPac1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rheMac2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rheMac2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rheMac2.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rheMac2.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rheMac2.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rheMac2.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rheMac2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn3.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn3.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn3.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn3.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn3.knownGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn3.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn3.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn3.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn3.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn4.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn4.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn4.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn4.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn4.knownGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn4.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn4.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn4.sgpGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'rn4.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'sacCer1.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'sacCer2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'strPur1.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'strPur1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'strPur1.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'strPur1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'strPur2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'strPur2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'strPur2.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'strPur2.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'taeGut1.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'taeGut1.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'taeGut1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'taeGut1.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'taeGut1.refGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'taeGut1.xenoRefGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'tetNig1.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'tetNig1.geneid.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'tetNig1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'tetNig1.nscanGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'tetNig2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'xenTro1.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'xenTro2.ensGene.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'xenTro2.geneSymbol.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file 'xenTro2.genscan.LENGTH.Rd':
  ‘downloadLengthFromUCSC’

Missing link or links in Rd file '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 ... ERROR
Running examples in ‘geneLenDataBase-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: supportedGeneIDs
> ### Title: Supported Gene IDs
> ### Aliases: supportedGeneIDs
> 
> ### ** Examples
> 
> supportedGeneIDs()
Error in load_package_gracefully("txdbmaker", "starting with BioC 3.19, ",  : 
  Could not load package txdbmaker. Is it installed?

  Note that starting with BioC 3.19, calling supportedUCSCtables()
  requires the txdbmaker package. Please install it with:

    BiocManager::install("txdbmaker")
Calls: supportedGeneIDs ... do.call -> do.call -> <Anonymous> -> load_package_gracefully
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/geneLenDataBase.Rcheck/00check.log’
for details.


Installation output

geneLenDataBase.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL geneLenDataBase
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘geneLenDataBase’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (geneLenDataBase)

Tests output


Example timings

geneLenDataBase.Rcheck/geneLenDataBase-Ex.timings

nameusersystemelapsed
anoCar1.ensGene.LENGTH0.0760.0000.077
anoCar1.genscan.LENGTH0.0470.0010.048
anoCar1.xenoRefGene.LENGTH0.9070.0040.912
anoGam1.ensGene.LENGTH0.0610.0040.065
anoGam1.geneid.LENGTH0.0480.0000.048
anoGam1.genscan.LENGTH0.0440.0000.044
apiMel1.genscan.LENGTH0.0370.0010.038
apiMel2.ensGene.LENGTH0.0900.0030.092
apiMel2.geneid.LENGTH0.0490.0000.049
apiMel2.genscan.LENGTH0.0960.0030.099
aplCal1.xenoRefGene.LENGTH1.0290.0931.120
bosTau2.geneSymbol.LENGTH0.040.000.04
bosTau2.geneid.LENGTH0.2180.0030.222
bosTau2.genscan.LENGTH0.0810.0010.082
bosTau2.refGene.LENGTH0.0390.0000.039
bosTau2.sgpGene.LENGTH0.1020.0000.102
bosTau3.ensGene.LENGTH0.1060.0080.114
bosTau3.geneSymbol.LENGTH0.0340.0030.039
bosTau3.geneid.LENGTH0.1140.0050.118
bosTau3.genscan.LENGTH0.0700.0040.074
bosTau3.refGene.LENGTH0.0310.0030.034
bosTau3.sgpGene.LENGTH0.0880.0040.091
bosTau4.ensGene.LENGTH0.0990.0000.098
bosTau4.geneSymbol.LENGTH0.0280.0070.036
bosTau4.genscan.LENGTH0.0680.0000.068
bosTau4.nscanGene.LENGTH0.0310.0000.031
bosTau4.refGene.LENGTH0.0300.0030.034
braFlo1.xenoRefGene.LENGTH0.3720.0120.383
caeJap1.xenoRefGene.LENGTH0.3310.0120.343
caePb1.xenoRefGene.LENGTH0.4530.0050.456
caePb2.xenoRefGene.LENGTH0.4240.0040.428
caeRem2.xenoRefGene.LENGTH0.3950.0030.399
caeRem3.xenoRefGene.LENGTH0.3510.0070.360
calJac1.genscan.LENGTH0.0920.0000.093
calJac1.nscanGene.LENGTH0.1110.0030.115
calJac1.xenoRefGene.LENGTH0.7750.0070.782
canFam1.ensGene.LENGTH0.2040.0040.208
canFam1.geneSymbol.LENGTH0.0020.0030.005
canFam1.genscan.LENGTH0.0610.0000.061
canFam1.nscanGene.LENGTH0.0600.0040.063
canFam1.refGene.LENGTH0.0040.0020.005
canFam1.xenoRefGene.LENGTH0.5340.0020.536
canFam2.ensGene.LENGTH0.0930.0000.093
canFam2.geneSymbol.LENGTH0.0050.0000.006
canFam2.genscan.LENGTH0.0570.0000.057
canFam2.nscanGene.LENGTH0.0590.0030.063
canFam2.refGene.LENGTH0.0060.0010.006
canFam2.xenoRefGene.LENGTH0.5300.0030.534
cavPor3.ensGene.LENGTH0.0810.0040.085
cavPor3.genscan.LENGTH0.0950.0000.096
cavPor3.nscanGene.LENGTH0.1240.0030.128
cavPor3.xenoRefGene.LENGTH0.5320.0000.533
cb1.xenoRefGene.LENGTH0.3570.0050.361
cb3.xenoRefGene.LENGTH0.3040.0040.308
ce2.geneSymbol.LENGTH0.0670.0000.068
ce2.geneid.LENGTH0.0480.0080.056
ce2.refGene.LENGTH0.0640.0000.065
ce4.geneSymbol.LENGTH0.0670.0000.067
ce4.refGene.LENGTH0.0680.0000.068
ce4.xenoRefGene.LENGTH0.0740.0080.082
ce6.ensGene.LENGTH0.0790.0160.095
ce6.geneSymbol.LENGTH0.0640.0030.068
ce6.refGene.LENGTH0.0640.0000.064
ce6.xenoRefGene.LENGTH0.0740.0030.078
ci1.geneSymbol.LENGTH0.0050.0010.005
ci1.refGene.LENGTH0.0040.0000.004
ci1.xenoRefGene.LENGTH0.1560.0030.160
ci2.ensGene.LENGTH0.1810.0180.199
ci2.geneSymbol.LENGTH0.0030.0010.005
ci2.refGene.LENGTH0.0040.0000.004
ci2.xenoRefGene.LENGTH0.2490.0080.257
danRer3.ensGene.LENGTH0.0940.0000.094
danRer3.geneSymbol.LENGTH0.0530.0000.053
danRer3.refGene.LENGTH0.0480.0010.049
danRer4.ensGene.LENGTH0.1100.0020.112
danRer4.geneSymbol.LENGTH0.0540.0000.054
danRer4.genscan.LENGTH0.0580.0030.062
danRer4.nscanGene.LENGTH0.0810.0050.085
danRer4.refGene.LENGTH0.0490.0000.049
danRer5.ensGene.LENGTH0.1120.0000.112
danRer5.geneSymbol.LENGTH0.0450.0040.049
danRer5.refGene.LENGTH0.0460.0000.046
danRer5.vegaGene.LENGTH0.0480.0000.048
danRer5.vegaPseudoGene.LENGTH0.0030.0000.003
danRer6.ensGene.LENGTH0.1070.0000.107
danRer6.geneSymbol.LENGTH0.050.000.05
danRer6.refGene.LENGTH0.0460.0000.046
danRer6.xenoRefGene.LENGTH0.4680.0000.468
dm1.geneSymbol.LENGTH0.0640.0000.064
dm1.genscan.LENGTH0.0250.0000.025
dm1.refGene.LENGTH0.0580.0000.058
dm2.geneSymbol.LENGTH0.0650.0000.065
dm2.geneid.LENGTH0.0360.0000.036
dm2.genscan.LENGTH0.0200.0040.024
dm2.nscanGene.LENGTH0.0470.0030.050
dm2.refGene.LENGTH0.0540.0050.058
dm3.geneSymbol.LENGTH0.0710.0000.071
dm3.nscanPasaGene.LENGTH0.0520.0000.052
dm3.refGene.LENGTH0.0670.0000.067
dp2.genscan.LENGTH0.0330.0000.033
dp2.xenoRefGene.LENGTH0.190.000.19
dp3.geneid.LENGTH0.0360.0030.040
dp3.genscan.LENGTH0.0270.0010.027
dp3.xenoRefGene.LENGTH0.1090.0000.109
droAna1.geneid.LENGTH0.0650.0030.069
droAna1.genscan.LENGTH0.0230.0000.023
droAna1.xenoRefGene.LENGTH0.2040.0000.204
droAna2.genscan.LENGTH0.050.000.05
droAna2.xenoRefGene.LENGTH0.4020.0020.403
droEre1.genscan.LENGTH0.0280.0010.030
droEre1.xenoRefGene.LENGTH0.2500.0030.254
droGri1.genscan.LENGTH0.0360.0040.040
droGri1.xenoRefGene.LENGTH0.2540.0150.270
droMoj1.geneid.LENGTH0.1200.0040.124
droMoj1.genscan.LENGTH0.0550.0000.055
droMoj1.xenoRefGene.LENGTH0.2160.0000.216
droMoj2.genscan.LENGTH0.0370.0000.037
droMoj2.xenoRefGene.LENGTH0.2650.0030.268
droPer1.genscan.LENGTH0.0370.0050.041
droPer1.xenoRefGene.LENGTH0.2770.0000.278
droSec1.genscan.LENGTH0.0270.0030.031
droSec1.xenoRefGene.LENGTH0.2620.0010.262
droSim1.geneid.LENGTH0.0380.0000.038
droSim1.genscan.LENGTH0.0250.0000.025
droSim1.xenoRefGene.LENGTH0.2310.0090.241
droVir1.geneid.LENGTH0.3200.0170.337
droVir1.genscan.LENGTH0.0380.0070.046
droVir1.xenoRefGene.LENGTH0.2330.0010.233
droVir2.genscan.LENGTH0.0370.0000.037
droVir2.xenoRefGene.LENGTH0.2650.0000.264
droYak1.geneid.LENGTH0.0460.0000.046
droYak1.genscan.LENGTH0.0310.0000.031
droYak1.xenoRefGene.LENGTH0.2110.0000.211
droYak2.genscan.LENGTH0.0290.0000.029
droYak2.xenoRefGene.LENGTH0.2470.0000.247
equCab1.geneSymbol.LENGTH0.0020.0030.005
equCab1.geneid.LENGTH0.0860.0050.090
equCab1.nscanGene.LENGTH0.0450.0000.044
equCab1.refGene.LENGTH0.0050.0000.005
equCab1.sgpGene.LENGTH0.0730.0000.072
equCab2.ensGene.LENGTH0.0970.0030.101
equCab2.geneSymbol.LENGTH0.0070.0010.008
equCab2.nscanGene.LENGTH0.0530.0000.053
equCab2.refGene.LENGTH0.0060.0000.007
equCab2.xenoRefGene.LENGTH0.5680.0040.572
felCat3.ensGene.LENGTH0.0970.0040.100
felCat3.geneSymbol.LENGTH0.0040.0000.004
felCat3.geneid.LENGTH1.2930.0951.388
felCat3.genscan.LENGTH0.1110.0000.111
felCat3.nscanGene.LENGTH0.0840.0000.083
felCat3.refGene.LENGTH0.0040.0000.004
felCat3.sgpGene.LENGTH0.1360.0000.135
felCat3.xenoRefGene.LENGTH0.9820.0050.986
fr1.ensGene.LENGTH0.0720.0000.073
fr1.genscan.LENGTH0.0570.0000.057
fr2.ensGene.LENGTH0.1220.0030.126
galGal2.ensGene.LENGTH0.0580.0000.058
galGal2.geneSymbol.LENGTH0.0170.0000.016
galGal2.geneid.LENGTH0.0390.0000.039
galGal2.genscan.LENGTH0.0520.0000.052
galGal2.refGene.LENGTH0.0160.0000.015
galGal2.sgpGene.LENGTH0.0460.0000.045
galGal3.ensGene.LENGTH0.0740.0000.074
galGal3.geneSymbol.LENGTH0.0120.0030.016
galGal3.genscan.LENGTH0.0480.0000.048
galGal3.nscanGene.LENGTH0.0720.0000.073
galGal3.refGene.LENGTH0.0130.0010.014
galGal3.xenoRefGene.LENGTH0.4330.0030.435
gasAcu1.ensGene.LENGTH0.0900.0000.091
gasAcu1.nscanGene.LENGTH0.0910.0070.099
hg16.acembly.LENGTH0.3490.0120.362
hg16.ensGene.LENGTH0.0780.0000.078
hg16.exoniphy.LENGTH0.2520.0050.257
hg16.geneSymbol.LENGTH0.1090.0030.111
hg16.geneid.LENGTH0.0490.0000.050
hg16.genscan.LENGTH0.0680.0000.069
hg16.knownGene.LENGTH0.1240.0040.128
hg16.refGene.LENGTH0.0990.0030.102
hg16.sgpGene.LENGTH0.0550.0030.059
hg17.acembly.LENGTH0.8720.0400.912
hg17.acescan.LENGTH0.0070.0040.010
hg17.ccdsGene.LENGTH0.0230.0000.023
hg17.ensGene.LENGTH0.1060.0000.107
hg17.exoniphy.LENGTH0.40.00.4
hg17.geneSymbol.LENGTH0.1020.0020.102
hg17.geneid.LENGTH0.0630.0100.073
hg17.genscan.LENGTH0.0560.0040.060
hg17.knownGene.LENGTH0.1050.0050.108
hg17.refGene.LENGTH0.0930.0030.096
hg17.sgpGene.LENGTH0.0720.0010.072
hg17.vegaGene.LENGTH0.0420.0000.041
hg17.vegaPseudoGene.LENGTH0.0170.0000.018
hg17.xenoRefGene.LENGTH0.2000.0000.201
hg18.acembly.LENGTH0.5780.0070.586
hg18.acescan.LENGTH0.0100.0020.010
hg18.ccdsGene.LENGTH0.0320.0040.035
hg18.ensGene.LENGTH0.1930.0020.196
hg18.exoniphy.LENGTH0.4660.0000.466
hg18.geneSymbol.LENGTH0.0980.0040.102
hg18.geneid.LENGTH0.0760.0000.076
hg18.genscan.LENGTH0.0620.0010.061
hg18.knownGene.LENGTH1.1980.0991.297
hg18.knownGeneOld3.LENGTH0.0600.0040.065
hg18.refGene.LENGTH0.0910.0000.091
hg18.sgpGene.LENGTH0.0740.0000.073
hg18.sibGene.LENGTH0.3070.0000.307
hg18.xenoRefGene.LENGTH0.3060.0000.306
hg19.ccdsGene.LENGTH0.0390.0000.039
hg19.ensGene.LENGTH0.2730.0000.274
hg19.exoniphy.LENGTH0.3860.0030.390
hg19.geneSymbol.LENGTH0.0930.0040.097
hg19.knownGene.LENGTH0.1630.0000.164
hg19.nscanGene.LENGTH0.1420.0000.143
hg19.refGene.LENGTH0.0950.0030.098
hg19.xenoRefGene.LENGTH0.3340.0000.333
loxAfr3.xenoRefGene.LENGTH0.6810.0000.680
mm7.ensGene.LENGTH0.1060.0000.106
mm7.geneSymbol.LENGTH0.0890.0000.090
mm7.geneid.LENGTH0.0710.0040.074
mm7.genscan.LENGTH0.0620.0000.062
mm7.knownGene.LENGTH0.0910.0000.092
mm7.refGene.LENGTH0.0810.0000.081
mm7.sgpGene.LENGTH0.0730.0040.076
mm7.xenoRefGene.LENGTH0.2790.0040.282
mm8.ccdsGene.LENGTH0.0220.0000.022
mm8.ensGene.LENGTH0.0670.0080.075
mm8.geneSymbol.LENGTH0.0860.0000.085
mm8.geneid.LENGTH0.0760.0000.075
mm8.genscan.LENGTH0.0570.0000.057
mm8.knownGene.LENGTH0.0900.0000.091
mm8.nscanGene.LENGTH0.0560.0030.059
mm8.refGene.LENGTH0.0790.0040.082
mm8.sgpGene.LENGTH0.0760.0000.075
mm8.sibGene.LENGTH0.2350.0080.243
mm8.xenoRefGene.LENGTH0.3440.0000.345
mm9.acembly.LENGTH0.3190.0080.327
mm9.ccdsGene.LENGTH0.0300.0000.031
mm9.ensGene.LENGTH0.1540.0000.155
mm9.exoniphy.LENGTH0.4210.0160.437
mm9.geneSymbol.LENGTH0.0750.0280.103
mm9.geneid.LENGTH0.0880.0040.092
mm9.genscan.LENGTH0.0640.0000.063
mm9.knownGene.LENGTH0.1050.0040.109
mm9.nscanGene.LENGTH0.0610.0030.065
mm9.refGene.LENGTH0.0860.0010.086
mm9.sgpGene.LENGTH0.0870.0000.086
mm9.xenoRefGene.LENGTH0.3430.0030.346
monDom1.genscan.LENGTH0.0650.0000.065
monDom4.ensGene.LENGTH0.0750.0000.075
monDom4.geneSymbol.LENGTH0.0000.0030.004
monDom4.genscan.LENGTH0.0540.0000.055
monDom4.nscanGene.LENGTH0.0560.0000.056
monDom4.refGene.LENGTH0.0040.0000.004
monDom4.xenoRefGene.LENGTH0.3280.0080.336
monDom5.ensGene.LENGTH0.1060.0030.109
monDom5.geneSymbol.LENGTH0.0040.0000.004
monDom5.genscan.LENGTH0.0580.0000.058
monDom5.nscanGene.LENGTH0.3930.0040.396
monDom5.refGene.LENGTH0.0040.0000.004
monDom5.xenoRefGene.LENGTH0.5760.0020.577
ornAna1.ensGene.LENGTH0.0920.0020.095
ornAna1.geneSymbol.LENGTH0.0030.0000.002
ornAna1.refGene.LENGTH0.0000.0030.002
ornAna1.xenoRefGene.LENGTH0.5220.0100.531
oryLat2.ensGene.LENGTH0.0860.0000.087
oryLat2.geneSymbol.LENGTH0.0040.0000.004
oryLat2.refGene.LENGTH0.0040.0000.004
oryLat2.xenoRefGene.LENGTH0.4650.0000.466
panTro1.ensGene.LENGTH0.1070.0070.116
panTro1.geneid.LENGTH0.0540.0000.054
panTro1.genscan.LENGTH0.0650.0000.065
panTro1.xenoRefGene.LENGTH0.1050.0030.108
panTro2.ensGene.LENGTH0.1130.0000.114
panTro2.geneSymbol.LENGTH0.0990.0000.099
panTro2.genscan.LENGTH0.0570.0060.061
panTro2.nscanGene.LENGTH0.0620.0020.065
panTro2.refGene.LENGTH0.0990.0000.099
panTro2.xenoRefGene.LENGTH0.4720.0000.472
petMar1.xenoRefGene.LENGTH0.2450.0040.250
ponAbe2.ensGene.LENGTH0.0820.0030.087
ponAbe2.geneSymbol.LENGTH0.0080.0040.012
ponAbe2.genscan.LENGTH0.0640.0000.064
ponAbe2.nscanGene.LENGTH0.0600.0000.061
ponAbe2.refGene.LENGTH0.0120.0000.011
ponAbe2.xenoRefGene.LENGTH0.5790.0000.578
priPac1.xenoRefGene.LENGTH0.3340.0000.333
rheMac2.ensGene.LENGTH0.1230.0060.129
rheMac2.geneSymbol.LENGTH0.0040.0010.005
rheMac2.geneid.LENGTH0.0750.0000.074
rheMac2.nscanGene.LENGTH0.0560.0060.061
rheMac2.refGene.LENGTH0.0040.0020.005
rheMac2.sgpGene.LENGTH0.0710.0010.070
rheMac2.xenoRefGene.LENGTH0.4290.0050.434
rn3.ensGene.LENGTH0.0960.0060.102
rn3.geneSymbol.LENGTH0.0510.0000.052
rn3.geneid.LENGTH0.0480.0040.052
rn3.genscan.LENGTH0.0620.0020.063
rn3.knownGene.LENGTH0.0230.0020.024
rn3.nscanGene.LENGTH0.060.000.06
rn3.refGene.LENGTH0.050.000.05
rn3.sgpGene.LENGTH0.0580.0010.057
rn3.xenoRefGene.LENGTH0.510.000.51
rn4.ensGene.LENGTH0.1350.0000.135
rn4.geneSymbol.LENGTH0.0450.0070.053
rn4.geneid.LENGTH0.0870.0000.087
rn4.genscan.LENGTH0.0610.0000.062
rn4.knownGene.LENGTH0.0240.0000.025
rn4.nscanGene.LENGTH0.0500.0030.055
rn4.refGene.LENGTH0.0470.0000.048
rn4.sgpGene.LENGTH0.0780.0040.082
rn4.xenoRefGene.LENGTH0.3210.0040.324
sacCer1.ensGene.LENGTH0.0190.0000.019
sacCer2.ensGene.LENGTH0.0130.0040.017
strPur1.geneSymbol.LENGTH0.0050.0000.004
strPur1.genscan.LENGTH0.0640.0020.065
strPur1.refGene.LENGTH0.0030.0020.005
strPur1.xenoRefGene.LENGTH0.6400.0040.645
strPur2.geneSymbol.LENGTH0.0040.0000.004
strPur2.genscan.LENGTH0.1080.0020.109
strPur2.refGene.LENGTH0.0010.0020.004
strPur2.xenoRefGene.LENGTH0.6120.0040.616