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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings customProDB_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/customProDB.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘customProDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘customProDB’ version ‘1.46.0’
* 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 ‘customProDB’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackage’ by ‘txdbmaker::makeTxDbPackage’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTables’ by ‘txdbmaker::supportedUCSCFeatureDbTables’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGFF’ by ‘txdbmaker::makeTxDbFromGFF’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromBiomart’ by ‘txdbmaker::makeTxDbPackageFromBiomart’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::supportedMiRBaseBuildValues’ by ‘txdbmaker::supportedMiRBaseBuildValues’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTracks’ by ‘txdbmaker::supportedUCSCFeatureDbTracks’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::browseUCSCtrack’ by ‘txdbmaker::browseUCSCtrack’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::getChromInfoFromBiomart’ by ‘txdbmaker::getChromInfoFromBiomart’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGRanges’ by ‘txdbmaker::makeTxDbFromGRanges’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::supportedUCSCtables’ by ‘txdbmaker::supportedUCSCtables’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromBiomart’ by ‘txdbmaker::makeTxDbFromBiomart’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::UCSCFeatureDbTableSchema’ by ‘txdbmaker::UCSCFeatureDbTableSchema’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromEnsembl’ by ‘txdbmaker::makeTxDbFromEnsembl’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::makeTxDb’ by ‘txdbmaker::makeTxDb’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::makeFDbPackageFromUCSC’ by ‘txdbmaker::makeFDbPackageFromUCSC’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromUCSC’ by ‘txdbmaker::makeTxDbFromUCSC’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromUCSC’ by ‘txdbmaker::makeTxDbPackageFromUCSC’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::makePackageName’ by ‘txdbmaker::makePackageName’ when loading ‘customProDB’
  Warning: replacing previous import ‘GenomicFeatures::makeFeatureDbFromUCSC’ by ‘txdbmaker::makeFeatureDbFromUCSC’ when loading ‘customProDB’
See ‘/home/biocbuild/bbs-3.20-bioc/meat/customProDB.Rcheck/00install.out’ for details.
* 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:
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  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 ... NOTE
Bed2Range: no visible binding for global variable ‘V5’
OutputNovelJun: no visible binding for global variable ‘jun_type’
OutputVarproseq: no visible binding for global variable ‘genename’
OutputVarproseq: no visible binding for global variable ‘txname’
OutputVarproseq: no visible binding for global variable ‘proname’
OutputVarproseq: no visible binding for global variable ‘aaref’
OutputVarproseq: no visible binding for global variable ‘aapos’
OutputVarproseq: no visible binding for global variable ‘aavar’
OutputVarproseq: no visible binding for global variable ‘rsid’
OutputVarproseq_single: no visible binding for global variable
  ‘genename’
OutputVarproseq_single: no visible binding for global variable ‘txname’
OutputVarproseq_single: no visible binding for global variable
  ‘proname’
OutputVarproseq_single: no visible binding for global variable ‘aaref’
OutputVarproseq_single: no visible binding for global variable ‘aapos’
OutputVarproseq_single: no visible binding for global variable ‘aavar’
OutputVarproseq_single: no visible binding for global variable ‘rsid’
Outputaberrant: no visible binding for global variable ‘pro_name’
Positionincoding: no visible binding for global variable ‘cds_start’
Positionincoding: no visible binding for global variable ‘cds_end’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘ensembl_gene_id’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘pro_name’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘chrom’
PrepareAnnotationEnsembl: no visible binding for global variable ‘name’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘alleleCount’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘alleles’
PrepareAnnotationRefseq: no visible binding for global variable ‘name’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘mrnaAcc’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘protAcc’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘transcript’
PrepareAnnotationRefseq: no visible binding for global variable ‘chrom’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘alleleCount’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘alleles’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘COSMIC’
Varlocation: no visible binding for global variable ‘pro_name’
Undefined global functions or variables:
  COSMIC V5 aapos aaref aavar alleleCount alleles cds_end cds_start
  chrom ensembl_gene_id genename jun_type mrnaAcc name pro_name proname
  protAcc rsid transcript txname
* 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 ‘customProDB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PrepareAnnotationEnsembl
> ### Title: prepare annotation from ENSEMBL
> ### Aliases: PrepareAnnotationEnsembl
> 
> ### ** Examples
> 
> 
> ensembl <- useEnsembl(biomart = 'genes', 
+  dataset = 'hsapiens_gene_ensembl',
+  version = 111)
> 
> annotation_path <- tempdir()
> transcript_ids <- c("ENST00000234420", "ENST00000269305", "ENST00000445888", 
+     "ENST00000257430", "ENST00000508376", "ENST00000288602", 
+     "ENST00000269571", "ENST00000256078", "ENST00000384871")
> 
> PrepareAnnotationEnsembl(mart=ensembl, annotation_path=annotation_path, 
+     splice_matrix=FALSE, dbsnp=NULL, transcript_ids=transcript_ids, 
+     COSMIC=FALSE)
Prepare gene/transcript/protein id mapping information (ids.RData) ...  done
Build TranscriptDB object (txdb.sqlite) ... 
Error in curl::curl_parse_url(url, baseurl = base_url, decode = FALSE) : 
  Failed to parse URL: Bad scheme
Calls: PrepareAnnotationEnsembl ... .useMart -> .cleanHostURL -> <Anonymous> -> <Anonymous>
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: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/customProDB.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL customProDB
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘customProDB’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackage’ by ‘txdbmaker::makeTxDbPackage’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTables’ by ‘txdbmaker::supportedUCSCFeatureDbTables’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGFF’ by ‘txdbmaker::makeTxDbFromGFF’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromBiomart’ by ‘txdbmaker::makeTxDbPackageFromBiomart’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::supportedMiRBaseBuildValues’ by ‘txdbmaker::supportedMiRBaseBuildValues’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTracks’ by ‘txdbmaker::supportedUCSCFeatureDbTracks’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::browseUCSCtrack’ by ‘txdbmaker::browseUCSCtrack’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::getChromInfoFromBiomart’ by ‘txdbmaker::getChromInfoFromBiomart’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGRanges’ by ‘txdbmaker::makeTxDbFromGRanges’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::supportedUCSCtables’ by ‘txdbmaker::supportedUCSCtables’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromBiomart’ by ‘txdbmaker::makeTxDbFromBiomart’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::UCSCFeatureDbTableSchema’ by ‘txdbmaker::UCSCFeatureDbTableSchema’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromEnsembl’ by ‘txdbmaker::makeTxDbFromEnsembl’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDb’ by ‘txdbmaker::makeTxDb’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeFDbPackageFromUCSC’ by ‘txdbmaker::makeFDbPackageFromUCSC’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromUCSC’ by ‘txdbmaker::makeTxDbFromUCSC’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromUCSC’ by ‘txdbmaker::makeTxDbPackageFromUCSC’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makePackageName’ by ‘txdbmaker::makePackageName’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeFeatureDbFromUCSC’ by ‘txdbmaker::makeFeatureDbFromUCSC’ when loading ‘customProDB’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackage’ by ‘txdbmaker::makeTxDbPackage’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTables’ by ‘txdbmaker::supportedUCSCFeatureDbTables’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGFF’ by ‘txdbmaker::makeTxDbFromGFF’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromBiomart’ by ‘txdbmaker::makeTxDbPackageFromBiomart’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::supportedMiRBaseBuildValues’ by ‘txdbmaker::supportedMiRBaseBuildValues’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTracks’ by ‘txdbmaker::supportedUCSCFeatureDbTracks’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::browseUCSCtrack’ by ‘txdbmaker::browseUCSCtrack’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::getChromInfoFromBiomart’ by ‘txdbmaker::getChromInfoFromBiomart’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGRanges’ by ‘txdbmaker::makeTxDbFromGRanges’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::supportedUCSCtables’ by ‘txdbmaker::supportedUCSCtables’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromBiomart’ by ‘txdbmaker::makeTxDbFromBiomart’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::UCSCFeatureDbTableSchema’ by ‘txdbmaker::UCSCFeatureDbTableSchema’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromEnsembl’ by ‘txdbmaker::makeTxDbFromEnsembl’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDb’ by ‘txdbmaker::makeTxDb’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeFDbPackageFromUCSC’ by ‘txdbmaker::makeFDbPackageFromUCSC’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromUCSC’ by ‘txdbmaker::makeTxDbFromUCSC’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromUCSC’ by ‘txdbmaker::makeTxDbPackageFromUCSC’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makePackageName’ by ‘txdbmaker::makePackageName’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeFeatureDbFromUCSC’ by ‘txdbmaker::makeFeatureDbFromUCSC’ when loading ‘customProDB’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackage’ by ‘txdbmaker::makeTxDbPackage’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTables’ by ‘txdbmaker::supportedUCSCFeatureDbTables’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGFF’ by ‘txdbmaker::makeTxDbFromGFF’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromBiomart’ by ‘txdbmaker::makeTxDbPackageFromBiomart’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::supportedMiRBaseBuildValues’ by ‘txdbmaker::supportedMiRBaseBuildValues’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTracks’ by ‘txdbmaker::supportedUCSCFeatureDbTracks’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::browseUCSCtrack’ by ‘txdbmaker::browseUCSCtrack’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::getChromInfoFromBiomart’ by ‘txdbmaker::getChromInfoFromBiomart’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGRanges’ by ‘txdbmaker::makeTxDbFromGRanges’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::supportedUCSCtables’ by ‘txdbmaker::supportedUCSCtables’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromBiomart’ by ‘txdbmaker::makeTxDbFromBiomart’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::UCSCFeatureDbTableSchema’ by ‘txdbmaker::UCSCFeatureDbTableSchema’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromEnsembl’ by ‘txdbmaker::makeTxDbFromEnsembl’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDb’ by ‘txdbmaker::makeTxDb’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeFDbPackageFromUCSC’ by ‘txdbmaker::makeFDbPackageFromUCSC’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromUCSC’ by ‘txdbmaker::makeTxDbFromUCSC’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromUCSC’ by ‘txdbmaker::makeTxDbPackageFromUCSC’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makePackageName’ by ‘txdbmaker::makePackageName’ when loading ‘customProDB’
Warning: replacing previous import ‘GenomicFeatures::makeFeatureDbFromUCSC’ by ‘txdbmaker::makeFeatureDbFromUCSC’ when loading ‘customProDB’
** testing if installed package keeps a record of temporary installation path
* DONE (customProDB)