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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IdMappingRetrieval.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IdMappingRetrieval_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/IdMappingRetrieval.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IdMappingRetrieval/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IdMappingRetrieval’ version ‘1.36.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IdMappingRetrieval’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'IdMappingRetrieval' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/IdMappingRetrieval.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  addServices.ServiceManager getDataFrame.Annotation
  getDataFrameList.ServiceManager getFolderName.Annotation
  getIdMap.Annotation getIdMapList.ServiceManager
  getServiceRoot.Annotation getServices.ServiceManager
  setOptions.Annotation setServices.ServiceManager
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘IdMappingRetrieval-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addServices.ServiceManager
> ### Title: Add services to the ServiceManager object
> ### Aliases: addServices.ServiceManager ServiceManager.addServices
> ###   addServices.ServiceManager addServices,ServiceManager-method
> ### Keywords: internal methods
> 
> ### ** Examples
> 
>  #create empty service manager object
>  svm<-ServiceManager(ServiceManager$getDefaultServices());
>  print(names(getServices(svm)))
Error in UseMethod("getServices") : 
  no applicable method for 'getServices' applied to an object of class "c('ServiceManager', 'Object')"
Calls: print -> getServices
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/IdMappingRetrieval.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IdMappingRetrieval
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘IdMappingRetrieval’ ...
** using staged installation
** R
** demo
** 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
Warning: Package 'IdMappingRetrieval' is deprecated and will be removed from
  Bioconductor version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'IdMappingRetrieval' is deprecated and will be removed from
  Bioconductor version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (IdMappingRetrieval)