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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings customProDB_1.50.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/customProDB.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘customProDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘customProDB’ version ‘1.50.0’
* 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-3.22-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)
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. └─biomaRt::useEnsembl(...)
  2.   └─biomaRt:::.listMarts(...)
  3.     └─biomaRt:::bmRequest(...)
  4.       └─httr2::req_perform(request)
  5.         └─httr2:::handle_resp(req, resp, error_call = error_call)
  6.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
  7.             ├─rlang::catch_cnd(...)
  8.             │ ├─rlang::eval_bare(...)
  9.             │ ├─base::tryCatch(...)
 10.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 13.             │ └─base::force(expr)
 14.             └─rlang::abort(...)
Execution halted
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/customProDB.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL customProDB
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘customProDB’ ...
** this is package ‘customProDB’ version ‘1.50.0’
** 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)