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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomeInfoDb_1.7.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GenomeInfoDb.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK
* this is package ‘GenomeInfoDb’ version ‘1.7.6’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomeInfoDb’ can be installed ... [7s/7s] OK
* checking installed package size ... NOTE
installed size is 20.7Mb
sub-directories of 1Mb or more:
data 20.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘BiocGenerics’ ‘S4Vectors’
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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘utils:::.roman2numeric’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.checkForAValidTaxonomyId: no visible global function definition for
‘data’
.fetch_assembly_report_from_URL: no visible global function definition
for ‘read.table’
.fetch_assembly_summary: no visible global function definition for
‘download.file’
.fetch_assembly_summary: no visible global function definition for
‘read.table’
.getDataInFile: no visible global function definition for ‘read.table’
.getNamedFiles: no visible global function definition for ‘setNames’
.getTaxonomyId: no visible global function definition for ‘data’
.lookupSpeciesFromTaxId: no visible global function definition for
‘data’
.lookupSpeciesFromTaxId: no visible binding for global variable
‘specData’
.processTaxNamesFile: no visible global function definition for
‘read.delim’
.supportedSeqnameMappings: no visible binding for global variable
‘read.table’
available.species: no visible global function definition for ‘data’
fetch_ChromInfo_from_UCSC: no visible global function definition for
‘download.file’
fetch_ChromInfo_from_UCSC: no visible global function definition for
‘read.table’
genomeStyles: no visible binding for global variable ‘read.table’
Undefined global functions or variables:
data download.file read.delim read.table setNames specData
Consider adding
importFrom("stats", "setNames")
importFrom("utils", "data", "download.file", "read.delim",
"read.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'seqinfo.Rd':
‘[GenomicRanges]{SummarizedExperiment}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/53s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
availableSpecies 11.288 0.242 11.557
speciesMap 6.113 0.209 6.337
GenomeDescription-class 4.838 0.128 5.117
seqinfo 2.188 0.120 5.312
fetchExtendedChromInfoFromUCSC 0.956 0.162 16.174
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.R’ [8s/8s]
[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
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/GenomeInfoDb.Rcheck/00check.log’
for details.
