Package: IdMappingRetrieval

Version: 1.32.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IdMappingRetrieval.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IdMappingRetrieval_1.32.0.tar.gz

StartedAt: 2019-10-16 02:28:00 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:30:03 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 122.9 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingRetrieval.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IdMappingRetrieval.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IdMappingRetrieval_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/IdMappingRetrieval.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.32.0’
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/IdMappingRetrieval.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL IdMappingRetrieval
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (IdMappingRetrieval)

name	user	system	elapsed
AnnotationEnsembl	0.001	0.000	0.000
AnnotationEnsemblCsv	0	0	0
AnnotationEnvision	0	0	0
addServices.ServiceManager	0.045	0.000	0.045
getDataFrame.Annotation	0	0	0
getDataFrameList.ServiceManager	0.001	0.000	0.000
getIdMap.Annotation	0.001	0.000	0.000
getIdMapList.ServiceManager	0.001	0.000	0.000
getServices.ServiceManager	0.007	0.003	0.010
setOptions.Annotation	0.000	0.000	0.001
setServices.ServiceManager	0.013	0.000	0.013
subsetByColumn	0	0	0