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