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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.