Back to Build/check report for BioC 3.19 experimental data
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This page was generated on 2024-05-02 14:51:33 -0400 (Thu, 02 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
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: 2024-05-02 07:30:02 -0400 (Thu, 02 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: 2024-05-02 11:56:23 -0400 (Thu, 02 May 2024)
EndedAt: 2024-05-02 12:05:05 -0400 (Thu, 02 May 2024)
EllapsedTime: 522.0 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 beta (2024-04-15 r86425)
* 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.LENGTH0.0780.0040.082
anoCar1.genscan.LENGTH0.050.000.05
anoCar1.xenoRefGene.LENGTH0.8830.0120.896
anoGam1.ensGene.LENGTH0.0610.0000.060
anoGam1.geneid.LENGTH0.0470.0000.046
anoGam1.genscan.LENGTH0.0430.0000.043
apiMel1.genscan.LENGTH0.0360.0010.038
apiMel2.ensGene.LENGTH0.0850.0070.091
apiMel2.geneid.LENGTH0.0490.0000.050
apiMel2.genscan.LENGTH0.1010.0040.105
aplCal1.xenoRefGene.LENGTH1.0980.0921.191
bosTau2.geneSymbol.LENGTH0.0350.0040.040
bosTau2.geneid.LENGTH0.2250.0000.226
bosTau2.genscan.LENGTH0.0820.0000.082
bosTau2.refGene.LENGTH0.0360.0040.039
bosTau2.sgpGene.LENGTH0.1120.0000.112
bosTau3.ensGene.LENGTH0.0950.0120.106
bosTau3.geneSymbol.LENGTH0.0320.0040.036
bosTau3.geneid.LENGTH0.1150.0000.116
bosTau3.genscan.LENGTH0.0650.0080.073
bosTau3.refGene.LENGTH0.0310.0040.035
bosTau3.sgpGene.LENGTH0.0900.0000.091
bosTau4.ensGene.LENGTH0.0940.0040.098
bosTau4.geneSymbol.LENGTH0.0350.0000.036
bosTau4.genscan.LENGTH0.0670.0000.067
bosTau4.nscanGene.LENGTH0.0310.0000.031
bosTau4.refGene.LENGTH0.0340.0000.034
braFlo1.xenoRefGene.LENGTH0.3980.0080.407
caeJap1.xenoRefGene.LENGTH0.3540.0040.359
caePb1.xenoRefGene.LENGTH0.4540.0080.462
caePb2.xenoRefGene.LENGTH0.4520.0040.456
caeRem2.xenoRefGene.LENGTH0.4170.0000.416
caeRem3.xenoRefGene.LENGTH0.3620.0000.362
calJac1.genscan.LENGTH0.0890.0040.093
calJac1.nscanGene.LENGTH0.1100.0040.114
calJac1.xenoRefGene.LENGTH0.7960.0000.797
canFam1.ensGene.LENGTH0.2240.0040.229
canFam1.geneSymbol.LENGTH0.0060.0000.005
canFam1.genscan.LENGTH0.0620.0000.062
canFam1.nscanGene.LENGTH0.0630.0000.064
canFam1.refGene.LENGTH0.0050.0000.006
canFam1.xenoRefGene.LENGTH0.5690.0080.578
canFam2.ensGene.LENGTH0.0920.0040.096
canFam2.geneSymbol.LENGTH0.0050.0010.005
canFam2.genscan.LENGTH0.0540.0030.057
canFam2.nscanGene.LENGTH0.0630.0000.063
canFam2.refGene.LENGTH0.0060.0000.005
canFam2.xenoRefGene.LENGTH0.5410.0000.541
cavPor3.ensGene.LENGTH0.0840.0000.085
cavPor3.genscan.LENGTH0.0950.0000.096
cavPor3.nscanGene.LENGTH0.1260.0040.130
cavPor3.xenoRefGene.LENGTH0.5700.0040.574
cb1.xenoRefGene.LENGTH0.4020.0000.402
cb3.xenoRefGene.LENGTH0.3280.0050.334
ce2.geneSymbol.LENGTH0.0680.0110.077
ce2.geneid.LENGTH0.0660.0040.070
ce2.refGene.LENGTH0.0690.0000.070
ce4.geneSymbol.LENGTH0.0660.0040.071
ce4.refGene.LENGTH0.0630.0000.063
ce4.xenoRefGene.LENGTH0.0790.0040.082
ce6.ensGene.LENGTH0.0980.0000.097
ce6.geneSymbol.LENGTH0.0660.0040.070
ce6.refGene.LENGTH0.0660.0000.066
ce6.xenoRefGene.LENGTH0.0820.0000.082
ci1.geneSymbol.LENGTH0.0050.0000.006
ci1.refGene.LENGTH0.0050.0000.005
ci1.xenoRefGene.LENGTH0.1730.0000.173
ci2.ensGene.LENGTH0.2100.0040.215
ci2.geneSymbol.LENGTH0.0050.0000.005
ci2.refGene.LENGTH0.0040.0000.005
ci2.xenoRefGene.LENGTH0.2680.0010.270
danRer3.ensGene.LENGTH0.0960.0020.097
danRer3.geneSymbol.LENGTH0.0550.0000.056
danRer3.refGene.LENGTH0.0500.0000.051
danRer4.ensGene.LENGTH0.1150.0040.119
danRer4.geneSymbol.LENGTH0.0480.0050.053
danRer4.genscan.LENGTH0.0610.0030.062
danRer4.nscanGene.LENGTH0.0870.0040.090
danRer4.refGene.LENGTH0.0520.0000.052
danRer5.ensGene.LENGTH0.1150.0000.115
danRer5.geneSymbol.LENGTH0.0450.0040.050
danRer5.refGene.LENGTH0.0460.0000.046
danRer5.vegaGene.LENGTH0.0470.0010.048
danRer5.vegaPseudoGene.LENGTH0.0010.0030.002
danRer6.ensGene.LENGTH0.1070.0040.111
danRer6.geneSymbol.LENGTH0.0500.0000.051
danRer6.refGene.LENGTH0.0440.0040.047
danRer6.xenoRefGene.LENGTH0.4830.0080.491
dm1.geneSymbol.LENGTH0.0610.0040.065
dm1.genscan.LENGTH0.0200.0080.027
dm1.refGene.LENGTH0.0630.0000.062
dm2.geneSymbol.LENGTH0.0620.0040.065
dm2.geneid.LENGTH0.0370.0000.036
dm2.genscan.LENGTH0.0250.0000.024
dm2.nscanGene.LENGTH0.0490.0040.053
dm2.refGene.LENGTH0.0560.0040.060
dm3.geneSymbol.LENGTH0.0720.0000.072
dm3.nscanPasaGene.LENGTH0.0520.0000.052
dm3.refGene.LENGTH0.0660.0000.067
dp2.genscan.LENGTH0.0290.0040.032
dp2.xenoRefGene.LENGTH0.1990.0040.202
dp3.geneid.LENGTH0.0410.0000.040
dp3.genscan.LENGTH0.0270.0000.027
dp3.xenoRefGene.LENGTH0.1110.0000.112
droAna1.geneid.LENGTH0.0690.0000.070
droAna1.genscan.LENGTH0.0220.0000.023
droAna1.xenoRefGene.LENGTH0.2030.0000.204
droAna2.genscan.LENGTH0.0490.0000.050
droAna2.xenoRefGene.LENGTH0.4090.0040.414
droEre1.genscan.LENGTH0.0310.0000.032
droEre1.xenoRefGene.LENGTH0.2540.0040.259
droGri1.genscan.LENGTH0.0420.0000.043
droGri1.xenoRefGene.LENGTH0.2900.0000.291
droMoj1.geneid.LENGTH0.1360.0000.136
droMoj1.genscan.LENGTH0.0590.0000.059
droMoj1.xenoRefGene.LENGTH0.2150.0040.219
droMoj2.genscan.LENGTH0.0390.0000.039
droMoj2.xenoRefGene.LENGTH0.30.00.3
droPer1.genscan.LENGTH0.0420.0000.043
droPer1.xenoRefGene.LENGTH0.3030.0000.303
droSec1.genscan.LENGTH0.0330.0040.036
droSec1.xenoRefGene.LENGTH0.2850.0040.289
droSim1.geneid.LENGTH0.0400.0000.041
droSim1.genscan.LENGTH0.0270.0000.027
droSim1.xenoRefGene.LENGTH0.2360.0000.236
droVir1.geneid.LENGTH0.3060.0120.318
droVir1.genscan.LENGTH0.0430.0000.043
droVir1.xenoRefGene.LENGTH0.2320.0000.232
droVir2.genscan.LENGTH0.0330.0040.037
droVir2.xenoRefGene.LENGTH0.2560.0000.256
droYak1.geneid.LENGTH0.0450.0000.045
droYak1.genscan.LENGTH0.0270.0040.030
droYak1.xenoRefGene.LENGTH0.2050.0000.205
droYak2.genscan.LENGTH0.0290.0000.029
droYak2.xenoRefGene.LENGTH0.2440.0050.249
equCab1.geneSymbol.LENGTH0.0030.0030.005
equCab1.geneid.LENGTH0.0870.0040.090
equCab1.nscanGene.LENGTH0.0430.0000.043
equCab1.refGene.LENGTH0.0050.0000.005
equCab1.sgpGene.LENGTH0.0700.0040.074
equCab2.ensGene.LENGTH0.10.00.1
equCab2.geneSymbol.LENGTH0.0070.0000.007
equCab2.nscanGene.LENGTH0.0530.0000.053
equCab2.refGene.LENGTH0.0070.0000.006
equCab2.xenoRefGene.LENGTH0.5760.0010.577
felCat3.ensGene.LENGTH0.1110.0070.117
felCat3.geneSymbol.LENGTH0.0040.0000.004
felCat3.geneid.LENGTH1.4000.1321.532
felCat3.genscan.LENGTH0.1050.0040.109
felCat3.nscanGene.LENGTH0.0880.0000.089
felCat3.refGene.LENGTH0.0040.0000.003
felCat3.sgpGene.LENGTH0.1420.0000.141
felCat3.xenoRefGene.LENGTH1.0250.0081.033
fr1.ensGene.LENGTH0.0760.0000.076
fr1.genscan.LENGTH0.0590.0040.064
fr2.ensGene.LENGTH0.1270.0040.130
galGal2.ensGene.LENGTH0.0550.0040.058
galGal2.geneSymbol.LENGTH0.0170.0000.016
galGal2.geneid.LENGTH0.0390.0000.039
galGal2.genscan.LENGTH0.0480.0040.053
galGal2.refGene.LENGTH0.0160.0000.016
galGal2.sgpGene.LENGTH0.0460.0000.045
galGal3.ensGene.LENGTH0.0710.0040.074
galGal3.geneSymbol.LENGTH0.0120.0040.016
galGal3.genscan.LENGTH0.0480.0000.048
galGal3.nscanGene.LENGTH0.0690.0000.069
galGal3.refGene.LENGTH0.0100.0040.014
galGal3.xenoRefGene.LENGTH0.4410.0000.441
gasAcu1.ensGene.LENGTH0.0900.0040.093
gasAcu1.nscanGene.LENGTH0.0970.0000.097
hg16.acembly.LENGTH0.3580.0040.362
hg16.ensGene.LENGTH0.0770.0000.077
hg16.exoniphy.LENGTH0.2490.0040.253
hg16.geneSymbol.LENGTH0.1060.0000.106
hg16.geneid.LENGTH0.050.000.05
hg16.genscan.LENGTH0.0670.0000.068
hg16.knownGene.LENGTH0.1270.0000.126
hg16.refGene.LENGTH0.1100.0040.114
hg16.sgpGene.LENGTH0.0620.0000.062
hg17.acembly.LENGTH0.8790.0200.899
hg17.acescan.LENGTH0.0070.0040.010
hg17.ccdsGene.LENGTH0.0230.0000.023
hg17.ensGene.LENGTH0.1030.0000.104
hg17.exoniphy.LENGTH0.3850.0010.386
hg17.geneSymbol.LENGTH0.0980.0030.099
hg17.geneid.LENGTH0.0720.0000.072
hg17.genscan.LENGTH0.0590.0000.059
hg17.knownGene.LENGTH0.1030.0000.103
hg17.refGene.LENGTH0.0930.0000.093
hg17.sgpGene.LENGTH0.0690.0000.068
hg17.vegaGene.LENGTH0.0410.0000.040
hg17.vegaPseudoGene.LENGTH0.0170.0000.017
hg17.xenoRefGene.LENGTH0.1940.0080.201
hg18.acembly.LENGTH0.5280.0240.552
hg18.acescan.LENGTH0.0110.0000.010
hg18.ccdsGene.LENGTH0.0350.0000.035
hg18.ensGene.LENGTH0.1920.0040.195
hg18.exoniphy.LENGTH0.4430.0040.446
hg18.geneSymbol.LENGTH0.1050.0000.105
hg18.geneid.LENGTH0.0780.0010.079
hg18.genscan.LENGTH0.0600.0030.062
hg18.knownGene.LENGTH1.2010.0561.257
hg18.knownGeneOld3.LENGTH0.0660.0040.069
hg18.refGene.LENGTH0.0900.0040.094
hg18.sgpGene.LENGTH0.0750.0000.075
hg18.sibGene.LENGTH0.3080.0040.312
hg18.xenoRefGene.LENGTH0.3020.0070.310
hg19.ccdsGene.LENGTH0.0390.0000.039
hg19.ensGene.LENGTH0.2720.0000.272
hg19.exoniphy.LENGTH0.3980.0000.398
hg19.geneSymbol.LENGTH0.0950.0040.099
hg19.knownGene.LENGTH0.1640.0040.168
hg19.nscanGene.LENGTH0.1380.0040.141
hg19.refGene.LENGTH0.0990.0000.099
hg19.xenoRefGene.LENGTH0.3310.0000.331
loxAfr3.xenoRefGene.LENGTH0.6770.0040.681
mm7.ensGene.LENGTH0.1030.0040.107
mm7.geneSymbol.LENGTH0.0860.0000.086
mm7.geneid.LENGTH0.0760.0000.076
mm7.genscan.LENGTH0.0600.0040.064
mm7.knownGene.LENGTH0.0920.0000.091
mm7.refGene.LENGTH0.0790.0040.083
mm7.sgpGene.LENGTH0.0760.0010.077
mm7.xenoRefGene.LENGTH0.2800.0030.282
mm8.ccdsGene.LENGTH0.0220.0000.022
mm8.ensGene.LENGTH0.0760.0000.076
mm8.geneSymbol.LENGTH0.0820.0040.085
mm8.geneid.LENGTH0.0760.0000.076
mm8.genscan.LENGTH0.0580.0000.058
mm8.knownGene.LENGTH0.090.000.09
mm8.nscanGene.LENGTH0.0560.0040.060
mm8.refGene.LENGTH0.0820.0000.081
mm8.sgpGene.LENGTH0.0760.0000.075
mm8.sibGene.LENGTH0.2450.0040.249
mm8.xenoRefGene.LENGTH0.360.000.36
mm9.acembly.LENGTH0.3040.0040.308
mm9.ccdsGene.LENGTH0.0250.0040.028
mm9.ensGene.LENGTH0.1420.0000.142
mm9.exoniphy.LENGTH0.4260.0160.442
mm9.geneSymbol.LENGTH0.0920.0040.095
mm9.geneid.LENGTH0.0850.0040.089
mm9.genscan.LENGTH0.0590.0050.064
mm9.knownGene.LENGTH0.1090.0030.112
mm9.nscanGene.LENGTH0.0610.0010.064
mm9.refGene.LENGTH0.0820.0000.082
mm9.sgpGene.LENGTH0.0850.0000.085
mm9.xenoRefGene.LENGTH0.3490.0080.357
monDom1.genscan.LENGTH0.0670.0000.067
monDom4.ensGene.LENGTH0.0750.0000.074
monDom4.geneSymbol.LENGTH0.0040.0000.004
monDom4.genscan.LENGTH0.0510.0040.055
monDom4.nscanGene.LENGTH0.0550.0000.055
monDom4.refGene.LENGTH0.0030.0000.003
monDom4.xenoRefGene.LENGTH0.3330.0000.332
monDom5.ensGene.LENGTH0.110.000.11
monDom5.geneSymbol.LENGTH0.0040.0000.004
monDom5.genscan.LENGTH0.0570.0000.057
monDom5.nscanGene.LENGTH0.3990.0080.407
monDom5.refGene.LENGTH0.0030.0000.004
monDom5.xenoRefGene.LENGTH0.5670.0040.570
ornAna1.ensGene.LENGTH0.0940.0160.110
ornAna1.geneSymbol.LENGTH0.0030.0000.003
ornAna1.refGene.LENGTH0.0030.0000.002
ornAna1.xenoRefGene.LENGTH0.5060.0120.518
oryLat2.ensGene.LENGTH0.0770.0080.085
oryLat2.geneSymbol.LENGTH0.0040.0000.004
oryLat2.refGene.LENGTH0.0030.0010.004
oryLat2.xenoRefGene.LENGTH0.4610.0030.463
panTro1.ensGene.LENGTH0.1070.0000.107
panTro1.geneid.LENGTH0.0530.0000.053
panTro1.genscan.LENGTH0.0640.0010.065
panTro1.xenoRefGene.LENGTH0.1120.0030.114
panTro2.ensGene.LENGTH0.1110.0000.112
panTro2.geneSymbol.LENGTH0.10.00.1
panTro2.genscan.LENGTH0.0620.0000.062
panTro2.nscanGene.LENGTH0.0620.0000.062
panTro2.refGene.LENGTH0.0960.0010.097
panTro2.xenoRefGene.LENGTH0.4640.0030.466
petMar1.xenoRefGene.LENGTH0.2430.0010.244
ponAbe2.ensGene.LENGTH0.0830.0020.085
ponAbe2.geneSymbol.LENGTH0.0130.0000.013
ponAbe2.genscan.LENGTH0.0640.0000.064
ponAbe2.nscanGene.LENGTH0.0570.0030.061
ponAbe2.refGene.LENGTH0.0120.0000.012
ponAbe2.xenoRefGene.LENGTH0.5810.0000.581
priPac1.xenoRefGene.LENGTH0.3230.0090.333
rheMac2.ensGene.LENGTH0.1350.0020.136
rheMac2.geneSymbol.LENGTH0.0060.0000.006
rheMac2.geneid.LENGTH0.0770.0000.077
rheMac2.nscanGene.LENGTH0.0620.0010.063
rheMac2.refGene.LENGTH0.0030.0030.005
rheMac2.sgpGene.LENGTH0.0680.0050.073
rheMac2.xenoRefGene.LENGTH0.4280.0030.430
rn3.ensGene.LENGTH0.1020.0000.102
rn3.geneSymbol.LENGTH0.0510.0000.051
rn3.geneid.LENGTH0.0470.0040.051
rn3.genscan.LENGTH0.0630.0000.063
rn3.knownGene.LENGTH0.0240.0000.024
rn3.nscanGene.LENGTH0.060.000.06
rn3.refGene.LENGTH0.0460.0030.050
rn3.sgpGene.LENGTH0.0570.0000.057
rn3.xenoRefGene.LENGTH0.4840.0040.488
rn4.ensGene.LENGTH0.1290.0000.129
rn4.geneSymbol.LENGTH0.0530.0000.053
rn4.geneid.LENGTH0.0860.0000.087
rn4.genscan.LENGTH0.060.000.06
rn4.knownGene.LENGTH0.0250.0000.025
rn4.nscanGene.LENGTH0.0550.0000.055
rn4.refGene.LENGTH0.0480.0000.048
rn4.sgpGene.LENGTH0.0810.0000.081
rn4.xenoRefGene.LENGTH0.3090.0000.309
sacCer1.ensGene.LENGTH0.0190.0000.019
sacCer2.ensGene.LENGTH0.0170.0000.017
strPur1.geneSymbol.LENGTH0.0040.0000.004
strPur1.genscan.LENGTH0.0610.0040.065
strPur1.refGene.LENGTH0.0040.0000.004
strPur1.xenoRefGene.LENGTH0.6490.0000.649
strPur2.geneSymbol.LENGTH0.0040.0000.004
strPur2.genscan.LENGTH0.1070.0000.107
strPur2.refGene.LENGTH0.0030.0000.003
strPur2.xenoRefGene.LENGTH0.5640.0000.564