BioC 3.5: CHECK report for metagenomeFeatures on veracruz2

Package: metagenomeFeatures

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeFeatures_1.8.1.tar.gz

StartedAt: 2017-10-18 05:51:48 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:55:52 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 244.2 seconds

RetCode: 0

Status:  OK

CheckDir: metagenomeFeatures.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 metagenomeFeatures_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/metagenomeFeatures.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeFeatures/DESCRIPTION’ ... OK
* this is package ‘metagenomeFeatures’ version ‘1.8.1’
* 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  8.7Mb
  sub-directories of 1Mb or more:
    extdata   6.7Mb
* 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
.mgDb_annotateFeatures: no visible binding for global variable
  ‘db_keys’
.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’
vignette_pheno_data: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  . Keys db_keys index read.csv
Consider adding
  importFrom("utils", "read.csv")
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 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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	0.235	0.010	0.251
aggregate_taxa	1.976	0.060	2.091
annotateFeatures-MgDb-method	0.496	0.022	0.530
annotateMRexp_fData-MgDb-method	0.000	0.000	0.001
get_demoMgDb	0.083	0.006	0.093
get_mockMgDb	0.092	0.004	0.098
mgF_meta	0.020	0.010	0.032
mgF_seq	0.127	0.002	0.135
mgF_taxa	0.033	0.002	0.040
mgF_tree	0.021	0.000	0.026
mgFeatures-class	0.001	0.000	0.002
mgQuery	0.001	0.001	0.002
mgdb_meta	0.082	0.003	0.087
mgdb_seq	0.134	0.003	0.141
mgdb_taxa	0.551	0.010	0.570
mgdb_tree	0.097	0.004	0.101
mock_mgF	0.002	0.001	0.002
mock_query_df	0.002	0.000	0.007
select-MgDb-method	0.734	0.031	0.785
taxa_columns	0.082	0.003	0.088
taxa_keys	0.101	0.004	0.109
taxa_keytypes	0.083	0.003	0.089
taxa_levels	0.128	0.015	0.148