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###
### Running command:
###
###   /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_1.2.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/txdbmaker.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘txdbmaker/DESCRIPTION’ ... OK
* this is package ‘txdbmaker’ version ‘1.2.1’
* 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: makeTxDbFromBiomart
> ### Title: Make a TxDb object from annotations available on a BioMart
> ###   database
> ### Aliases: makeTxDbFromBiomart getChromInfoFromBiomart
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## A. BASIC USAGE
> ## ---------------------------------------------------------------------
> 
> ## We can use listDatasets() from the biomaRt package to list the
> ## datasets available in the "ENSEMBL_MART_ENSEMBL" BioMart database:
> library(biomaRt)
> listMarts(host="https://www.ensembl.org")
               biomart                version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 113
2   ENSEMBL_MART_MOUSE      Mouse strains 113
3     ENSEMBL_MART_SNP  Ensembl Variation 113
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 113
> mart <- useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", host="https://www.ensembl.org")
> datasets <- listDatasets(mart)
> head(datasets)
                       dataset                           description
1 abrachyrhynchus_gene_ensembl Pink-footed goose genes (ASM259213v1)
2     acalliptera_gene_ensembl      Eastern happy genes (fAstCal1.3)
3   acarolinensis_gene_ensembl       Green anole genes (AnoCar2.0v2)
4    acchrysaetos_gene_ensembl       Golden eagle genes (bAquChr1.2)
5    acitrinellus_gene_ensembl        Midas cichlid genes (Midas_v5)
6    amelanoleuca_gene_ensembl       Giant panda genes (ASM200744v2)
      version
1 ASM259213v1
2  fAstCal1.3
3 AnoCar2.0v2
4  bAquChr1.2
5    Midas_v5
6 ASM200744v2
> subset(datasets, grepl("elegans", dataset, ignore.case=TRUE))
                 dataset                                            description
27 celegans_gene_ensembl Caenorhabditis elegans (Nematode, N2) genes (WBcel235)
    version
27 WBcel235
> 
> ## Retrieve the full transcript dataset for Worm:
> txdb1 <- makeTxDbFromBiomart(dataset="celegans_gene_ensembl")
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning in .infer_chrominfo_from_transcripts_and_splicings(transcripts$tx_chrom,  :
  chromosome lengths and circularity flags are not available for this
  TxDb object
OK
> txdb1
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Caenorhabditis elegans
# Taxonomy ID: 6239
# Resource URL: www.ensembl.org:443
# BioMart database: ENSEMBL_MART_ENSEMBL
# BioMart database version: Ensembl Genes 113
# BioMart dataset: celegans_gene_ensembl
# BioMart dataset description: Caenorhabditis elegans (Nematode, N2) genes (WBcel235)
# BioMart dataset version: WBcel235
# Full dataset: yes
# miRBase build ID: NA
# Nb of transcripts: 60000
# Db created by: txdbmaker package from Bioconductor
# Creation time: 2025-02-28 11:19:49 -0500 (Fri, 28 Feb 2025)
# txdbmaker version at creation time: 1.2.1
# RSQLite version at creation time: 2.3.9
# DBSCHEMAVERSION: 1.2
> 
> ## Retrieve an incomplete transcript dataset for Human:
> transcript_ids <- c(
+     "ENST00000013894",
+     "ENST00000268655",
+     "ENST00000313243",
+     "ENST00000435657",
+     "ENST00000384428",
+     "ENST00000478783"
+ )
> 
> if (interactive()) {
+   txdb2 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl",
+                                transcript_ids=transcript_ids)
+   txdb2  # note that these annotations match the GRCh38 genome assembly
+ }
> 
> ## ---------------------------------------------------------------------
> ## B. ACCESSING THE EnsemblGenomes MARTS
> ## ---------------------------------------------------------------------
> 
> library(biomaRt)
> 
> ## Note that BioMart is not currently available for Ensembl Bacteria.
> 
> ## ---------------------
> ## --- Ensembl Fungi ---
> 
> mart <- useEnsemblGenomes(biomart="fungi_mart")
> datasets <- listDatasets(mart)
> datasets$dataset
 [1] "aastaci_eg_gene"            "aclavatus_eg_gene"         
 [3] "aflavus_eg_gene"            "afumigatus_eg_gene"        
 [5] "afumigatusa1163_eg_gene"    "agossypii_eg_gene"         
 [7] "ainvadans_eg_gene"          "anidulans_eg_gene"         
 [9] "aniger_eg_gene"             "aoryzae_eg_gene"           
[11] "aterreus_eg_gene"           "bbassiana_eg_gene"         
[13] "bcinerea_eg_gene"           "bgraminis_eg_gene"         
[15] "calbicans_eg_gene"          "cauris_eg_gene"            
[17] "cduobushaemulonis_eg_gene"  "cglabrata_eg_gene"         
[19] "cgloeosporioides_eg_gene"   "cgraminicola_eg_gene"      
[21] "chaemuloni_eg_gene"         "chigginsianum_eg_gene"     
[23] "cneoformans_eg_gene"        "corbiculare_eg_gene"       
[25] "cparapsilosis_eg_gene"      "cpseudohaemulonis_eg_gene" 
[27] "ctropicalis_eg_gene"        "dseptosporum_eg_gene"      
[29] "fculmorum_eg_gene"          "ffujikuroi_eg_gene"        
[31] "fgraminearum_eg_gene"       "foxysporum_eg_gene"        
[33] "fpseudograminearum_eg_gene" "fsolani_eg_gene"           
[35] "fverticillioides_eg_gene"   "ggraminis_eg_gene"         
[37] "gultimum_eg_gene"           "hcapsulatum_eg_gene"       
[39] "kpastoris_eg_gene"          "lmaculans_eg_gene"         
[41] "mlaricipopulina_eg_gene"    "moryzae_eg_gene"           
[43] "mpoae_eg_gene"              "mviolaceum_eg_gene"        
[45] "ncrassa_eg_gene"            "nfischeri_eg_gene"         
[47] "pchrysosporium_eg_gene"     "pgraminis_eg_gene"         
[49] "pgraminisug99_eg_gene"      "pnodorum_eg_gene"          
[51] "poryzae_eg_gene"            "pstriiformis_eg_gene"      
[53] "pteres_eg_gene"             "ptriticina_eg_gene"        
[55] "ptriticirepentis_eg_gene"   "scerevisiae_eg_gene"       
[57] "scryophilus_eg_gene"        "sjaponicus_eg_gene"        
[59] "soctosporus_eg_gene"        "spombe_eg_gene"            
[61] "sreilianum_eg_gene"         "ssclerotiorum_eg_gene"     
[63] "tmelanosporum_eg_gene"      "treesei_eg_gene"           
[65] "tvirens_eg_gene"            "umaydis_eg_gene"           
[67] "vdahliae_eg_gene"           "vdahliaejr2_eg_gene"       
[69] "ylipolytica_eg_gene"        "ztritici_eg_gene"          
> yeast_txdb <- makeTxDbFromBiomart(biomart="fungi_mart",
+                                   dataset="scerevisiae_eg_gene",
+                                   host="https://fungi.ensembl.org")
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> yeast_txdb
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Saccharomyces cerevisiae
# Taxonomy ID: 4932
# Resource URL: fungi.ensembl.org:443
# BioMart database: fungi_mart
# BioMart database version: Ensembl Fungi Genes 60
# BioMart dataset: scerevisiae_eg_gene
# BioMart dataset description: Saccharomyces cerevisiae genes (R64-1-1)
# BioMart dataset version: R64-1-1
# Full dataset: yes
# miRBase build ID: NA
# Nb of transcripts: 7127
# Db created by: txdbmaker package from Bioconductor
# Creation time: 2025-02-28 11:20:16 -0500 (Fri, 28 Feb 2025)
# txdbmaker version at creation time: 1.2.1
# RSQLite version at creation time: 2.3.9
# DBSCHEMAVERSION: 1.2
> 
> ## -----------------------
> ## --- Ensembl Metazoa ---
> 
> ## The metazoa mart is slow and at the same time it doesn't seem to
> ## support requests that take more than 1 min at the moment. So a call to
> ## biomaRt::getBM() will fail with a "Timeout was reached" error if the
> ## requested data takes more than 1 min to download. This unfortunately
> ## happens with the example below so we don't try to run it for now.
> 
> ## ----------------------
> ## --- Ensembl Plants ---
> 
> ## Like the metazoa mart (see above), the plants mart is also slow and
> ## doesn't seem to support requests that take more than 1 min either.
> ## So we don't try to run the example below for now.
> 
> ## ------------------------
> ## --- Ensembl Protists ---
> 
> mart <- useEnsemblGenomes(biomart="protists_mart")
> datasets <- listDatasets(mart)
> datasets$dataset
 [1] "alaibachii_eg_gene"      "bnatans_eg_gene"        
 [3] "ddiscoideum_eg_gene"     "ehistolytica_eg_gene"   
 [5] "ehuxleyi_eg_gene"        "glamblia_eg_gene"       
 [7] "gtheta_eg_gene"          "harabidopsidis_eg_gene" 
 [9] "lmajor_eg_gene"          "paphanidermatum_eg_gene"
[11] "parrhenomanes_eg_gene"   "pberghei_eg_gene"       
[13] "pchabaudi_eg_gene"       "pfalciparum_eg_gene"    
[15] "pinfestans_eg_gene"      "pirregulare_eg_gene"    
[17] "piwayamai_eg_gene"       "pkernoviae_eg_gene"     
[19] "pknowlesi_eg_gene"       "plateralis_eg_gene"     
[21] "pmultistriata_eg_gene"   "pparasitica_eg_gene"    
[23] "pramorum_eg_gene"        "psojae_eg_gene"         
[25] "ptetraurelia_eg_gene"    "ptricornutum_eg_gene"   
[27] "pultimum_eg_gene"        "pvexans_eg_gene"        
[29] "pvivax_eg_gene"          "tbrucei_eg_gene"        
[31] "tgondii_eg_gene"         "tpseudonana_eg_gene"    
[33] "tthermophila_eg_gene"   
> tgondii_txdb <- makeTxDbFromBiomart(biomart="protists_mart",
+                                     dataset="tgondii_eg_gene",
+                                     host="https://protists.ensembl.org")
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> tgondii_txdb
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Toxoplasma gondii
# Taxonomy ID: 5811
# Resource URL: protists.ensembl.org:443
# BioMart database: protists_mart
# BioMart database version: Ensembl Protists Genes 60
# BioMart dataset: tgondii_eg_gene
# BioMart dataset description: Toxoplasma gondii ME49 genes (TGA4)
# BioMart dataset version: TGA4
# Full dataset: yes
# miRBase build ID: NA
# Nb of transcripts: 8920
# Db created by: txdbmaker package from Bioconductor
# Creation time: 2025-02-28 11:20:45 -0500 (Fri, 28 Feb 2025)
# txdbmaker version at creation time: 1.2.1
# RSQLite version at creation time: 2.3.9
# DBSCHEMAVERSION: 1.2
> 
> ## ---------------------------------------------------------------------
> ## C. USING AN Ensembl MIRROR
> ## ---------------------------------------------------------------------
> 
> ## You can use the 'host' argument to access the "ENSEMBL_MART_ENSEMBL"
> ## BioMart database at a mirror (e.g. at uswest.ensembl.org). A gotcha
> ## when doing this is that the name of the database on the mirror might
> ## be different! We can check this with listMarts() from the biomaRt
> ## package:
> if (interactive()) {
+ 
+   listMarts(host="https://useast.ensembl.org")
+ 
+   txdb3 <- makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
+                                dataset="hsapiens_gene_ensembl",
+                                transcript_ids=transcript_ids,
+                                host="https://useast.ensembl.org")
+   txdb3
+ }
> ## Therefore in addition to setting 'host' to "uswest.ensembl.org", we
> ## might also need to specify the 'biomart' argument.
> 
> 
> ## ---------------------------------------------------------------------
> ## D. USING FILTERS
> ## ---------------------------------------------------------------------
> 
> ## We can use listFilters() from the biomaRt package to get valid filter
> ## names:
> mart <- useEnsembl(biomart="ENSEMBL_MART_ENSEMBL",
+                 dataset="hsapiens_gene_ensembl",
+                 host="https://www.ensembl.org")
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.
Calls: useEnsembl -> useDataset -> checkDataset
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-3.20-bioc/meat/txdbmaker.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL txdbmaker
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘txdbmaker’ ...
** 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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, 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()
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... 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
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
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 -- Fri Feb 28 11:23:46 2025 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
txdbmaker RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
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 .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.
3: 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
> 
> proc.time()
   user  system elapsed 
145.694   3.388 175.533