BioC 3.5: CHECK report for biomformat on oaxaca

Package: biomformat

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biomformat_1.3.0.tar.gz

StartedAt: 2017-03-03 23:42:39 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:43:40 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 61.5 seconds

RetCode: 0

Status:  OK

CheckDir: biomformat.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biomformat_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/biomformat.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomformat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biomformat’ version ‘1.3.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biomformat’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
make_biom: no visible global function definition for ‘packageVersion’
namedList: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  packageVersion setNames
Consider adding
  importFrom("stats", "setNames")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-biomformat.R’
 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/biomformat.Rcheck/00check.log’
for details.

* installing *source* package ‘biomformat’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘biomformat’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘biomformat’
Creating a generic function for ‘rownames’ from package ‘base’ in package ‘biomformat’
Creating a generic function for ‘colnames’ from package ‘base’ in package ‘biomformat’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biomformat)

name	user	system	elapsed
biom-class	0.294	0.012	0.306
biom-methods	0.108	0.001	0.109
biom_data-methods	0.159	0.001	0.161
biom_shape-methods	0.003	0.000	0.003
colnames-methods	0.003	0.000	0.004
header-methods	0.003	0.000	0.004
make_biom	0.094	0.002	0.095
matrix_element_type-methods	0.003	0.000	0.003
ncol-methods	0.003	0.000	0.004
nrow-methods	0.003	0.000	0.003
observation_metadata-methods	0.034	0.002	0.036
read_biom	0.005	0.000	0.006
read_hdf5_biom	0.188	0.002	0.209
rownames-methods	0.004	0.001	0.003
sample_metadata-methods	0.023	0.001	0.025
show-methods	0.003	0.000	0.004
write_biom	0.009	0.001	0.009