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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IdMappingRetrieval.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings IdMappingRetrieval_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/IdMappingRetrieval.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'IdMappingRetrieval' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'IdMappingRetrieval' is deprecated and will be removed from
See 'C:/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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
** running examples for arch 'x64' ... 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: 2 ERRORs, 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/IdMappingRetrieval.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/IdMappingRetrieval_1.36.0.tar.gz && rm -rf IdMappingRetrieval.buildbin-libdir && mkdir IdMappingRetrieval.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IdMappingRetrieval.buildbin-libdir IdMappingRetrieval_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL IdMappingRetrieval_1.36.0.zip && rm IdMappingRetrieval_1.36.0.tar.gz IdMappingRetrieval_1.36.0.zip
###
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100 34876  100 34876    0     0   555k      0 --:--:-- --:--:-- --:--:--  619k

install for i386

* installing *source* package 'IdMappingRetrieval' ...
** using staged installation
** R
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'IdMappingRetrieval'
    finding HTML links ... done
    Annotation                              html  
    AnnotationAffx                          html  
    AnnotationEnsembl                       html  
    AnnotationEnsemblCsv                    html  
    AnnotationEnvision                      html  
    AnnotationNetAffx                       html  
    Generic.Roo                             html  
    IdMappingAnnotationData.root            html  
    IdMappingRetrieval-package              html  
    ServiceManager                          html  
    addServices.ServiceManager              html  
    as.IdMap                                html  
    as.UniquePairs                          html  
    filesExist.AnnotationNetAffx            html  
    getColumns.Annotation                   html  
    getColumns.AnnotationAffx               html  
    getColumns.AnnotationEnsembl            html  
    getColumns.AnnotationEnsemblCsv         html  
    getColumns.AnnotationEnvision           html  
    getDataFrame.Annotation                 html  
    getDataFrameList.ServiceManager         html  
    getFolderName.Annotation                html  
    getIdMap.Annotation                     html  
    getIdMapList.ServiceManager             html  
    getServiceRoot.Annotation               html  
    getServices.ServiceManager              html  
    readDF.Annotation                       html  
    readDF.AnnotationAffx                   html  
    readDF.AnnotationEnsembl                html  
    readDF.AnnotationEnsemblCsv             html  
    readDF.AnnotationEnvision               html  
    readDF.AnnotationNetAffx                html  
    setOptions.Annotation                   html  
    setServices.ServiceManager              html  
    subsetByColumn                          html  
    swapKeys                                html  
** 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

install for x64

* installing *source* package 'IdMappingRetrieval' ...
** testing if installed package can be loaded
Warning: Package 'IdMappingRetrieval' is deprecated and will be removed from
  Bioconductor version 3.12
* MD5 sums
packaged installation of 'IdMappingRetrieval' as IdMappingRetrieval_1.36.0.zip
* DONE (IdMappingRetrieval)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'IdMappingRetrieval' successfully unpacked and MD5 sums checked