BioC 3.3: CHECK report for polyester on morelia

Package: polyester

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings polyester_1.7.1.tar.gz

StartedAt: 2016-04-21 06:09:53 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 06:11:42 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 108.8 seconds

RetCode: 0

Status:  OK

CheckDir: polyester.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 polyester_1.7.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/polyester.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 ‘polyester/DESCRIPTION’ ... OK
* this is package ‘polyester’ version ‘1.7.1’
* 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 ‘polyester’ can be installed ... [7s/7s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.write_info: no visible global function definition for ‘write.table’
NB: no visible global function definition for ‘rnbinom’
add_gc_bias: no visible global function definition for ‘loess’
add_gc_bias: no visible global function definition for ‘predict’
add_platform_error: no visible global function definition for ‘data’
add_platform_error: no visible binding for global variable ‘model1’
add_platform_error: no visible binding for global variable ‘model2’
add_platform_error: no visible binding for global variable ‘model4’
add_platform_error: no visible binding for global variable ‘model5’
add_platform_error: no visible binding for global variable ‘model3’
add_platform_error: no visible binding for global variable ‘model6’
add_platform_error: no visible binding for global variable ‘model7’
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 ‘data’
generate_fragments: no visible binding for global variable
  ‘empirical_density’
generate_fragments: no visible global function definition for ‘rnorm’
generate_fragments: no visible global function definition for ‘runif’
generate_fragments: no visible binding for global variable ‘rnaf’
generate_fragments: no visible binding for global variable ‘cdnaf’
get_params: no visible global function definition for ‘smooth.spline’
process_custom: no visible global function definition for ‘read.table’
seq_gtf: no visible global function definition for ‘read.table’
simulate_experiment: no visible global function definition for ‘rnorm’
simulate_experiment_empirical: no visible global function definition
  for ‘texpr’
simulate_experiment_empirical: no visible global function definition
  for ‘model.matrix’
simulate_experiment_empirical: no visible global function definition
  for ‘write.table’
Undefined global functions or variables:
  cdnaf data empirical_density loess model.matrix model1 model2 model3
  model4 model5 model6 model7 predict rbinom read.table rnaf rnbinom
  rnorm runif smooth.spline texpr write.table
Consider adding
  importFrom("stats", "loess", "model.matrix", "predict", "rbinom",
             "rnbinom", "rnorm", "runif", "smooth.spline")
  importFrom("utils", "data", "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 ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
add_gc_bias         11.708  0.083  11.805
create_read_numbers  5.760  0.140   5.946
* 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-3.3-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	0.000	0.000	0.001
add_error	0.134	0.006	0.199
add_gc_bias	11.708	0.083	11.805
add_platform_error	0.316	0.017	0.335
count_transcripts	0.025	0.004	0.028
create_read_numbers	5.760	0.140	5.946
fpkm_to_counts	0.055	0.005	0.060
generate_fragments	0.324	0.021	0.361
getAttributeField	1.992	0.044	2.037
get_params	0.054	0.005	0.059
get_reads	0.168	0.005	0.173
reverse_complement	0.182	0.006	0.188
seq_gtf	0	0	0
simulate_experiment	0	0	0
simulate_experiment_countmat	0.001	0.000	0.000
simulate_experiment_empirical	0.001	0.000	0.001
write_reads	0.115	0.005	0.121