BioC 3.3: CHECK report for polyester on zin2

Package: polyester

Version: 1.8.3

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings polyester_1.8.3.tar.gz

StartedAt: 2016-10-13 05:19:13 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:20:30 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 77.8 seconds

RetCode: 0

Status:  OK

CheckDir: polyester.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings polyester_1.8.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/polyester.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘polyester/DESCRIPTION’ ... OK
* this is package ‘polyester’ version ‘1.8.3’
* 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 ‘polyester’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘limma’ ‘logspline’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: no visible global function definition for ‘rnbinom’
count_transcripts: no visible global function definition for
  ‘read.table’
create_read_numbers: no visible global function definition for
  ‘predict’
create_read_numbers: no visible global function definition for ‘rbinom’
create_read_numbers: no visible global function definition for
  ‘rnbinom’
generate_fragments: no visible global function definition for ‘rnorm’
generate_fragments: no visible global function definition for ‘runif’
get_params: no visible global function definition for ‘smooth.spline’
seq_gtf: no visible global function definition for ‘read.table’
simulate_experiment: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  predict rbinom read.table rnbinom rnorm runif smooth.spline
  write.table
Consider adding
  importFrom("stats", "predict", "rbinom", "rnbinom", "rnorm", "runif",
             "smooth.spline")
  importFrom("utils", "read.table", "write.table")
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
Examples with CPU or elapsed time > 5s
         user system elapsed
seq_gtf 5.748  0.052   7.244
* 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
  ‘/home/biocbuild/bbs-3.3-bioc/meat/polyester.Rcheck/00check.log’
for details.

* installing *source* package ‘polyester’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (polyester)

name	user	system	elapsed
NB	0.001	0.000	0.001
add_error	0.107	0.016	0.133
count_transcripts	0.034	0.004	0.037
create_read_numbers	4.683	0.143	4.843
fpkm_to_counts	0.057	0.004	0.061
generate_fragments	0.173	0.000	0.173
getAttributeField	1.384	0.000	1.398
get_params	0.062	0.000	0.063
get_reads	0.141	0.004	0.145
reverse_complement	0.176	0.000	0.176
seq_gtf	5.748	0.052	7.244
simulate_experiment	0.001	0.000	0.000
simulate_experiment_countmat	0	0	0
write_reads	0.090	0.008	0.098