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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:txdbmaker.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings txdbmaker_1.3.1.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/txdbmaker.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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")
Warning in getMethods(coerce, table = TRUE) :
  'getMethods' is deprecated.
Use 'getMethodsForDispatch(f, TRUE)' instead.
See help("Deprecated")
Warning in getMethods(coerce, table = TRUE) :
  'getMethods' is deprecated.
Use 'getMethodsForDispatch(f, TRUE)' instead.
See help("Deprecated")
Error in errorHandler(responseError) : Internal Server Error
Calls: UCSCFeatureDbTableSchema ... doTryCatch -> <Anonymous> -> handleResponse -> errorHandler
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 13 lines of output:
  txdbmaker RUnit Tests - 9 test functions, 1 error, 0 failures
  ERROR in test_makeTxDbFromBiomart: Error in checkDataset(dataset = dataset, mart = mart) : 
    The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
  
  Test files with failing tests
  
     test_makeTxDbFromBiomart.R 
       test_makeTxDbFromBiomart 
  
  
  Error in BiocGenerics:::testPackage("txdbmaker") : 
    unit tests failed for package txdbmaker
  Calls: <Anonymous> -> <Anonymous>
  In addition: There were 16 warnings (use warnings() to see them)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/txdbmaker.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL txdbmaker
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘txdbmaker’ ...
** this is package ‘txdbmaker’ version ‘1.3.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (txdbmaker)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("txdbmaker") || stop("unable to load txdbmaker package")
Loading required package: txdbmaker
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: GenomeInfoDb
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'txdbmaker'

The following objects are masked from 'package:GenomicFeatures':

    UCSCFeatureDbTableSchema, browseUCSCtrack, getChromInfoFromBiomart,
    makeFDbPackageFromUCSC, makeFeatureDbFromUCSC, makePackageName,
    makeTxDb, makeTxDbFromBiomart, makeTxDbFromEnsembl,
    makeTxDbFromGFF, makeTxDbFromGRanges, makeTxDbFromUCSC,
    makeTxDbPackage, makeTxDbPackageFromBiomart,
    makeTxDbPackageFromUCSC, supportedMiRBaseBuildValues,
    supportedUCSCFeatureDbTables, supportedUCSCFeatureDbTracks,
    supportedUCSCtables

[1] TRUE
> txdbmaker:::.test()
Timing stopped at: 0.718 0.05 1.2
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
In addition: Warning message:
In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning messages:
1: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type exon.
  This information was ignored.
2: In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
3: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
4: In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
5: In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
6: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID,  :
  the transcript names ("tx_name" column in the TxDb object) imported from the
  "Name" attribute are not unique
7: In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
8: In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
9: In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Error in x$.self$finalize() : attempt to apply non-function
Download the sgdGene table ... OK
Download the sgdIsoforms table ... OK
Download the sgdCanonical table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK


RUNIT TEST PROTOCOL -- Tue Mar  4 15:22:54 2025 
*********************************************** 
Number of test functions: 9 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
txdbmaker RUnit Tests - 9 test functions, 1 error, 0 failures
ERROR in test_makeTxDbFromBiomart: Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.

Test files with failing tests

   test_makeTxDbFromBiomart.R 
     test_makeTxDbFromBiomart 


Error in BiocGenerics:::testPackage("txdbmaker") : 
  unit tests failed for package txdbmaker
Calls: <Anonymous> -> <Anonymous>
In addition: There were 16 warnings (use warnings() to see them)
Execution halted