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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:txdbmaker.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings txdbmaker_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/txdbmaker.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘txdbmaker/DESCRIPTION’ ... OK
* this is package ‘txdbmaker’ version ‘1.3.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘txdbmaker’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘AnnotationDbi:::dbEasyQuery’ ‘BiocGenerics:::testPackage’
‘GenomeInfoDb:::check_tax_id’
‘GenomeInfoDb:::lookup_organism_by_tax_id’
‘GenomeInfoDb:::lookup_tax_id_by_organism’
‘GenomeInfoDb:::make_circ_flags_from_circ_seqs’
‘S4Vectors:::anyMissingOrOutside’
‘S4Vectors:::extract_data_frame_rows’ ‘S4Vectors:::quick_togroup’
‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
‘rtracklayer:::resourceDescription’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘txdbmaker-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeFeatureDbFromUCSC
> ### Title: Making a FeatureDb object from annotations available at the UCSC
> ### Genome Browser
> ### Aliases: supportedUCSCFeatureDbTracks supportedUCSCFeatureDbTables
> ### UCSCFeatureDbTableSchema makeFeatureDbFromUCSC
>
> ### ** Examples
>
> ## Display the list of genomes available at UCSC:
> library(UCSC.utils)
> list_UCSC_genomes()[ , "genome"]
[1] "ailMel1" "allMis1" "anoCar1" "anoCar2" "anoGam1"
[6] "anoGam3" "apiMel1" "apiMel2" "aplCal1" "aptMan1"
[11] "aquChr2" "balAcu1" "bisBis1" "bosTau2" "bosTau3"
[16] "bosTau4" "bosTau6" "bosTau7" "bosTau8" "bosTau9"
[21] "braFlo1" "caePb1" "caePb2" "cb1" "cb3"
[26] "ce2" "ce4" "ce6" "ce10" "ce11"
[31] "caeJap1" "caeRem2" "caeRem3" "calJac1" "calJac3"
[36] "calJac4" "calMil1" "canFam1" "canFam2" "canFam3"
[41] "canFam4" "canFam5" "canFam6" "cavPor3" "cerSim1"
[46] "chlSab2" "choHof1" "chrPic1" "ci1" "ci2"
[51] "ci3" "criGri1" "criGriChoV1" "criGriChoV2" "danRer3"
[56] "danRer4" "danRer5" "danRer6" "danRer7" "danRer10"
[61] "danRer11" "dasNov3" "dipOrd1" "droAna1" "droAna2"
[66] "droEre1" "droGri1" "dm1" "dm2" "dm3"
[71] "dm6" "droMoj1" "droMoj2" "droPer1" "dp2"
[76] "dp3" "droSec1" "droSim1" "droVir1" "droVir2"
[81] "droYak1" "droYak2" "echTel1" "echTel2" "enhLutNer1"
[86] "equCab1" "equCab2" "equCab3" "eriEur1" "eriEur2"
[91] "felCat3" "felCat4" "felCat5" "felCat8" "felCat9"
[96] "eboVir3" "gadMor1" "galVar1" "galGal2" "galGal3"
[101] "galGal4" "galGal5" "galGal6" "gasAcu1" "geoFor1"
[106] "gorGor3" "gorGor4" "gorGor5" "gorGor6" "hetGla1"
[111] "hetGla2" "hg16" "hg17" "hg18" "hg19"
[116] "hg38" "hs1" "latCha1" "loxAfr3" "macFas5"
[121] "rheMac2" "rheMac3" "rheMac8" "rheMac10" "macEug2"
[126] "manPen1" "melGal1" "melGal5" "melUnd1" "micMur1"
[131] "micMur2" "mpxvRivers" "monDom1" "monDom4" "monDom5"
[136] "mm7" "mm8" "mm9" "mm10" "mm39"
[141] "musFur1" "nanPar1" "nasLar1" "neoSch1" "nomLeu1"
[146] "nomLeu2" "nomLeu3" "ochPri2" "ochPri3" "oreNil2"
[151] "ornAna1" "ornAna2" "oryCun2" "oryLat2" "otoGar3"
[156] "oviAri1" "oviAri3" "oviAri4" "panPan1" "panPan2"
[161] "panPan3" "panTro1" "panTro2" "panTro3" "panTro4"
[166] "panTro5" "panTro6" "papAnu2" "papAnu4" "papHam1"
[171] "petMar1" "petMar2" "petMar3" "ponAbe2" "ponAbe3"
[176] "priPac1" "proCap1" "pteVam1" "rn3" "rn4"
[181] "rn5" "rn6" "rn7" "rhiRox1" "wuhCor1"
[186] "sacCer1" "sacCer2" "sacCer3" "saiBol1" "sarHar1"
[191] "sorAra1" "sorAra2" "speTri2" "strPur1" "strPur2"
[196] "susScr2" "susScr3" "susScr11" "taeGut1" "taeGut2"
[201] "fr1" "fr2" "fr3" "tarSyr1" "tarSyr2"
[206] "tetNig1" "tetNig2" "thaSir1" "triMan1" "tupBel1"
[211] "turTru2" "vicPac1" "vicPac2" "xenLae2" "xenTro1"
[216] "xenTro2" "xenTro3" "xenTro7" "xenTro9" "xenTro10"
>
> ## Display the list of Tracks supported by makeFeatureDbFromUCSC():
> # supportedUCSCFeatureDbTracks("mm10")
>
> ## Display the list of tables supported by your track:
> supportedUCSCFeatureDbTables(genome="mm10",
+ track="qPCR Primers")
[1] "qPcrPrimers"
>
> ## Display fields that could be passed in to colnames:
> UCSCFeatureDbTableSchema(genome="mm10",
+ track="qPCR Primers",
+ tablename="qPcrPrimers")
Error: unable to find an inherited method for function ‘trackNames’ for signature ‘object = "UCSCTableQuery"’
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/txdbmaker.Rcheck/00check.log’
for details.