BioC 3.3: CHECK report for metagenomeFeatures on oaxaca

Package: metagenomeFeatures

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeFeatures_1.2.2.tar.gz

StartedAt: 2016-10-13 03:31:00 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:34:06 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 186.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: metagenomeFeatures.Rcheck

Warnings: 3

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeFeatures_1.2.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/metagenomeFeatures.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeFeatures/DESCRIPTION’ ... OK
* this is package ‘metagenomeFeatures’ version ‘1.2.2’
* 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 ‘metagenomeFeatures’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 35.7Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata  34.3Mb
* 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 loading without being on the library search path ... 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
.select.taxa: no visible binding for global variable ‘Keys’
.select.taxa: no visible binding for global variable ‘.’
aggregate_taxa: no visible binding for global variable ‘.’
aggregate_taxa: no visible binding for global variable ‘index’
aggregate_taxa: no visible global function definition for
  ‘newMRexperiment’
Undefined global functions or variables:
  . Keys index newMRexperiment
* checking Rd files ... WARNING
checkRd: (5) aggregate_taxa.Rd:0-40: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'msd16s_query_df.Rd':
  ‘metagenomeAnnotation-class’ ‘annotate’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘msd16s_metagenomeAnnotation’
Undocumented data sets:
  ‘msd16s_metagenomeAnnotation’
Undocumented S4 methods:
  generic 'taxa_columns' and siglist 'MgDb'
  generic 'taxa_keys' and siglist 'MgDb'
  generic 'taxa_keytypes' and siglist 'MgDb'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 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.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: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/metagenomeFeatures.Rcheck/00check.log’
for details.

* installing *source* package ‘metagenomeFeatures’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metagenomeFeatures)

name	user	system	elapsed
MgDb-class	0.993	0.014	1.019
aggregate_taxa	0.001	0.000	0.001
get_demoMgDb	0.608	0.008	0.617
mgF_meta	0.001	0.000	0.001
mgF_seq	0.001	0.000	0.001
mgF_taxa	0.001	0.001	0.001
mgF_tree	0.001	0.000	0.000
mgFeatures-class	0.004	0.001	0.005
mgQuery	0.002	0.001	0.002
mgdb_meta	0	0	0
mgdb_seq	0	0	0
mgdb_taxa	0.000	0.000	0.001
mgdb_tree	0.001	0.000	0.001
msd16s_query_df	0.003	0.001	0.004
select-MgDb-method	0.810	0.028	0.888
taxa_columns	0.320	0.008	0.329
taxa_keys	0.339	0.006	0.345
taxa_keytypes	0.619	0.008	0.628
taxa_levels	0.000	0.000	0.001