##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OrganismDbi.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings OrganismDbi_1.49.0.tar.gz
###
##############################################################################
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/OrganismDbi.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OrganismDbi/DESCRIPTION' ... OK
* this is package 'OrganismDbi' version '1.49.0'
* 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 whether package 'OrganismDbi' 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 object imported by a ':::' call: 'BiocGenerics:::testPackage'
  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 ... NOTE
checkRd: (-1) coordinate-mapping-method.Rd:61-74: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coordinate-mapping-method.Rd: mapToTranscripts
  makeOrganismDbFromBiomart.Rd: supportedMiRBaseBuildValues
  makeOrganismDbFromUCSC.Rd: supportedMiRBaseBuildValues
  rangeBasedAccessors.Rd: extractTranscriptSeqs, GRangesList, id2name,
    exonsBy, Rle, IntegerRangesList, GenomicRanges, genes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 'OrganismDbi-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeOrganismDbFromBiomart
> ### Title: Make a OrganismDb object from annotations available on a BioMart
> ###   database
> ### Aliases: makeOrganismDbFromBiomart
> 
> ### ** Examples
> 
> ## Discover which datasets are available in the "ensembl" BioMart
> ## database:
> library(biomaRt)
> mart <- useEnsembl("ensembl")
Ensembl site unresponsive, trying asia mirror
> 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
> 
> ## Retrieving an incomplete transcript dataset for Human from the
> ## "ensembl" BioMart database:
> transcript_ids <- c(
+     "ENST00000013894",
+     "ENST00000268655",
+     "ENST00000313243",
+     "ENST00000435657",
+     "ENST00000384428",
+     "ENST00000478783"
+ )
> odb <- makeOrganismDbFromBiomart(transcript_ids=transcript_ids)
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: makeOrganismDbFromBiomart ... .useMart2 -> useEnsembl -> useDataset -> checkDataset
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
OrganismDb 9.31   0.43   12.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'OrganismDbi_unit_tests.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, 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/OrganismDbi.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL OrganismDbi
###
##############################################################################
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'OrganismDbi' ...
** 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 (OrganismDbi)

R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> BiocGenerics:::testPackage("OrganismDbi")

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

Welcome to Bioconductor

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


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

Loading required package: Homo.sapiens
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Loading required package: RSQLite
Loading required package: Rattus.norvegicus
Loading required package: org.Rn.eg.db

Loading required package: TxDb.Rnorvegicus.UCSC.rn5.refGene
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned many:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned many:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Loading required package: FDb.UCSC.tRNAs
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    FileForFormat

  403 genes were dropped because they have exons located on both strands of the
  same reference sequence or on more than one reference sequence, so cannot be
  represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
  object, or use suppressMessages() to suppress this message.


RUNIT TEST PROTOCOL -- Thu Nov 28 03:23:28 2024 
*********************************************** 
Number of test functions: 41 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
OrganismDbi RUnit Tests - 41 test functions, 0 errors, 0 failures
Number of test functions: 41 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: call dbDisconnect() when finished working with a connection 
2: In call_fun_in_txdbmaker("makePackageName", ...) :
  makePackageName() has moved from GenomicFeatures to the txdbmaker package,
  and is formally deprecated in GenomicFeatures >= 1.59.1. Please call
  txdbmaker::makePackageName() to get rid of this warning.
> 
> proc.time()
   user  system elapsed 
 311.40   16.31  341.45