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BioC 2.14: CHECK report for IdMappingRetrieval on morelia

This page was generated on 2014-10-08 09:04:58 -0700 (Wed, 08 Oct 2014).

Package 408/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IdMappingRetrieval 1.10.0
Alex Lisovich , Roger Day
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/IdMappingRetrieval
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: IdMappingRetrieval
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingRetrieval_1.10.0.tar.gz
StartedAt: 2014-10-07 23:34:00 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:37:01 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 181.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IdMappingRetrieval.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingRetrieval_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.10.0’
* 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 ... [19s/19s] WARNING
Found the following significant warnings:
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/createSubmission.AnnotationNetAffx.Rd:18: Section \synopsis is unrecognized and will be dropped
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getArrayType.Annotation.Rd:20: Section \synopsis is unrecognized and will be dropped
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getArrayTypes.Annotation.Rd:20: Section \synopsis is unrecognized and will be dropped
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getColumns1.AnnotationEnsembl.Rd:23: Section \synopsis is unrecognized and will be dropped
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getColumns2.AnnotationEnsembl.Rd:23: Section \synopsis is unrecognized and will be dropped
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getCredentials.Annotation.Rd:23: Section \synopsis is unrecognized and will be dropped
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getDefaultServices.ServiceManager.Rd:19: Section \synopsis is unrecognized and will be dropped
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getProbesetList.AnnotationAffx.Rd:19: Section \synopsis is unrecognized and will be dropped
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getRoot.Annotation.Rd:19: Section \synopsis is unrecognized and will be dropped
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/init.Annotation.Rd:24: Section \synopsis is unrecognized and will be dropped
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/setCredentials.Annotation.Rd:26: Section \synopsis is unrecognized and will be dropped
  Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/setCredentials.AnnotationAffx.Rd:20: Section \synopsis is unrecognized and will be dropped
See ‘/Users/biocbuild/bbs-2.14-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
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ENVISIONQuery’ ‘R.oo’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
* checking Rd files ... WARNING
prepare_Rd: createSubmission.AnnotationNetAffx.Rd:18: Section \synopsis is unrecognized and will be dropped
prepare_Rd: getArrayType.Annotation.Rd:20: Section \synopsis is unrecognized and will be dropped
prepare_Rd: getArrayTypes.Annotation.Rd:20: Section \synopsis is unrecognized and will be dropped
prepare_Rd: getColumns1.AnnotationEnsembl.Rd:23: Section \synopsis is unrecognized and will be dropped
prepare_Rd: getColumns2.AnnotationEnsembl.Rd:23: Section \synopsis is unrecognized and will be dropped
prepare_Rd: getCredentials.Annotation.Rd:23: Section \synopsis is unrecognized and will be dropped
prepare_Rd: getDefaultServices.ServiceManager.Rd:19: Section \synopsis is unrecognized and will be dropped
prepare_Rd: getProbesetList.AnnotationAffx.Rd:19: Section \synopsis is unrecognized and will be dropped
prepare_Rd: getRoot.Annotation.Rd:19: Section \synopsis is unrecognized and will be dropped
prepare_Rd: init.Annotation.Rd:24: Section \synopsis is unrecognized and will be dropped
prepare_Rd: setCredentials.Annotation.Rd:26: Section \synopsis is unrecognized and will be dropped
prepare_Rd: setCredentials.AnnotationAffx.Rd:20: Section \synopsis is unrecognized and will be dropped
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'createSubmission.AnnotationNetAffx' but not in code:
  $

Functions or methods with usage in documentation object 'getArrayType.Annotation' but not in code:
  $

Functions or methods with usage in documentation object 'getArrayTypes.Annotation' but not in code:
  $

Functions or methods with usage in documentation object 'getColumns1.AnnotationEnsembl' but not in code:
  $

Functions or methods with usage in documentation object 'getColumns2.AnnotationEnsembl' but not in code:
  $

Functions or methods with usage in documentation object 'getCredentials.Annotation' but not in code:
  $

Functions or methods with usage in documentation object 'getDefaultServices.ServiceManager' but not in code:
  $

Functions or methods with usage in documentation object 'getProbesetList.AnnotationAffx' but not in code:
  $

Functions or methods with usage in documentation object 'getRoot.Annotation' but not in code:
  $

Functions or methods with usage in documentation object 'init.Annotation' but not in code:
  $

Functions or methods with usage in documentation object 'setCredentials.Annotation' but not in code:
  $

Functions or methods with usage in documentation object 'setCredentials.AnnotationAffx' but not in code:
  $

Codoc mismatches from documentation object 'createSubmission.AnnotationNetAffx':
AnnotationNetAffx
  Code: function(cacheFolderName = "NetAffxCsv", primaryColumn =
                 "Probe.Set.ID", secondaryColumn = "SwissProt", swap =
                 TRUE, df_filename = NULL, ...)
  Docs: function()
  Argument names in code not in docs:
    cacheFolderName primaryColumn secondaryColumn swap df_filename ...
createSubmission
  Code: function(...)
  Docs: function()
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'getArrayType.Annotation':
Annotation
  Code: function(cacheFolderName = "", primaryColumn = "From",
                 secondaryColumn = "To", swap = FALSE, species = "Homo
                 sapiens", verbose = FALSE, ...)
  Docs: function()
  Argument names in code not in docs:
    cacheFolderName primaryColumn secondaryColumn swap species verbose
    ...
getArrayType
  Code: function(...)
  Docs: function()
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'getArrayTypes.Annotation':
Annotation
  Code: function(cacheFolderName = "", primaryColumn = "From",
                 secondaryColumn = "To", swap = FALSE, species = "Homo
                 sapiens", verbose = FALSE, ...)
  Docs: function()
  Argument names in code not in docs:
    cacheFolderName primaryColumn secondaryColumn swap species verbose
    ...
getArrayTypes
  Code: function(...)
  Docs: function()
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'getColumns1.AnnotationEnsembl':
AnnotationEnsembl
  Code: function(cacheFolderName = "Ensembl", primaryColumn =
                 c("uniprot_swissprot_accession", "uniprot_sptrembl"),
                 secondaryColumn = NA, swap = FALSE, species =
                 "hsapiens_gene_ensembl", full.merge = TRUE, ...)
  Docs: function()
  Argument names in code not in docs:
    cacheFolderName primaryColumn secondaryColumn swap species
    full.merge ...
getColumns1
  Code: function(...)
  Docs: function()
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'getColumns2.AnnotationEnsembl':
AnnotationEnsembl
  Code: function(cacheFolderName = "Ensembl", primaryColumn =
                 c("uniprot_swissprot_accession", "uniprot_sptrembl"),
                 secondaryColumn = NA, swap = FALSE, species =
                 "hsapiens_gene_ensembl", full.merge = TRUE, ...)
  Docs: function()
  Argument names in code not in docs:
    cacheFolderName primaryColumn secondaryColumn swap species
    full.merge ...
getColumns2
  Code: function(...)
  Docs: function()
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'getCredentials.Annotation':
Annotation
  Code: function(cacheFolderName = "", primaryColumn = "From",
                 secondaryColumn = "To", swap = FALSE, species = "Homo
                 sapiens", verbose = FALSE, ...)
  Docs: function()
  Argument names in code not in docs:
    cacheFolderName primaryColumn secondaryColumn swap species verbose
    ...
getCredentials
  Code: function(...)
  Docs: function()
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'getDefaultServices.ServiceManager':
ServiceManager
  Code: function(services = list(), ...)
  Docs: function()
  Argument names in code not in docs:
    services ...
getDefaultServices
  Code: function(...)
  Docs: function()
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'getProbesetList.AnnotationAffx':
AnnotationAffx
  Code: function(cacheFolderName = "Affymetrix", primaryColumn =
                 "Probe.Set.ID", secondaryColumn = "SwissProt", swap =
                 TRUE, ...)
  Docs: function()
  Argument names in code not in docs:
    cacheFolderName primaryColumn secondaryColumn swap ...
getProbesetList
  Code: function(...)
  Docs: function()
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'getRoot.Annotation':
Annotation
  Code: function(cacheFolderName = "", primaryColumn = "From",
                 secondaryColumn = "To", swap = FALSE, species = "Homo
                 sapiens", verbose = FALSE, ...)
  Docs: function()
  Argument names in code not in docs:
    cacheFolderName primaryColumn secondaryColumn swap species verbose
    ...
getRoot
  Code: function(...)
  Docs: function()
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'init.Annotation':
Annotation
  Code: function(cacheFolderName = "", primaryColumn = "From",
                 secondaryColumn = "To", swap = FALSE, species = "Homo
                 sapiens", verbose = FALSE, ...)
  Docs: function()
  Argument names in code not in docs:
    cacheFolderName primaryColumn secondaryColumn swap species verbose
    ...
init
  Code: function(...)
  Docs: function()
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'setCredentials.Annotation':
Annotation
  Code: function(cacheFolderName = "", primaryColumn = "From",
                 secondaryColumn = "To", swap = FALSE, species = "Homo
                 sapiens", verbose = FALSE, ...)
  Docs: function()
  Argument names in code not in docs:
    cacheFolderName primaryColumn secondaryColumn swap species verbose
    ...
setCredentials
  Code: function(...)
  Docs: function()
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'setCredentials.AnnotationAffx':
AnnotationAffx
  Code: function(cacheFolderName = "Affymetrix", primaryColumn =
                 "Probe.Set.ID", secondaryColumn = "SwissProt", swap =
                 TRUE, ...)
  Docs: function()
  Argument names in code not in docs:
    cacheFolderName primaryColumn secondaryColumn swap ...
setCredentials
  Code: function(...)
  Docs: function()
  Argument names in code not in docs:
    ...

* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] 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

WARNING: There were 3 warnings.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00check.log’
for details.

IdMappingRetrieval.Rcheck/00install.out:

* installing *source* package ‘IdMappingRetrieval’ ...
** R
** demo
** inst
** preparing package for lazy loading
This is  ENVISIONQuery   1.12.0   2013-08-20 
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function getServices to getServices.default, which was defined in environment ENVISIONQuery.
** help
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/createSubmission.AnnotationNetAffx.Rd:18: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getArrayType.Annotation.Rd:20: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getArrayTypes.Annotation.Rd:20: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getColumns1.AnnotationEnsembl.Rd:23: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getColumns2.AnnotationEnsembl.Rd:23: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getCredentials.Annotation.Rd:23: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getDefaultServices.ServiceManager.Rd:19: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getProbesetList.AnnotationAffx.Rd:19: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/getRoot.Annotation.Rd:19: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/init.Annotation.Rd:24: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/setCredentials.Annotation.Rd:26: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/IdMappingRetrieval.Rcheck/00_pkg_src/IdMappingRetrieval/man/setCredentials.AnnotationAffx.Rd:20: Section \synopsis is unrecognized and will be dropped
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
This is  ENVISIONQuery   1.12.0   2013-08-20 
* DONE (IdMappingRetrieval)

IdMappingRetrieval.Rcheck/IdMappingRetrieval-Ex.timings:

nameusersystemelapsed
AnnotationDavid0.0000.0000.001
AnnotationEnsembl0.0010.0000.001
AnnotationEnsemblCsv0.0010.0000.001
AnnotationEnvision0.0010.0000.001
addServices.ServiceManager0.0510.0010.051
createSubmission.AnnotationNetAffx0.0010.0000.000
getArrayType.Annotation0.0010.0000.001
getArrayTypes.Annotation0.0010.0010.000
getCredentials.Annotation0.0010.0000.001
getDataFrame.Annotation0.0000.0000.001
getDataFrameList.ServiceManager0.0010.0000.002
getDefaultServices.ServiceManager0.0180.0000.018
getIdMap.Annotation0.0010.0010.001
getIdMapList.ServiceManager0.0010.0000.001
getProbesetList.AnnotationAffx0.0010.0000.001
getRoot.Annotation0.0010.0010.001
getServiceRoot.Annotation0.0010.0000.001
getServices.ServiceManager0.0120.0000.012
init.Annotation000
setCredentials.Annotation0.0000.0000.001
setCredentials.AnnotationAffx000
setOptions.Annotation000
setServices.ServiceManager0.0160.0000.017
subsetByColumn0.0010.0000.000