Package: polyester

Version: 1.19.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:polyester.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings polyester_1.19.0.tar.gz

StartedAt: 2019-04-09 02:46:06 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:48:04 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 117.5 seconds

RetCode: 0

Status:  OK

CheckDir: polyester.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:polyester.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings polyester_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/polyester.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.19.0’
* 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 ‘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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zlibbioc’
  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
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’
generate_fragments: no visible binding for global variable
  ‘empirical_density’
generate_fragments: no visible binding for global variable ‘rnaf’
generate_fragments: no visible binding for global variable ‘cdnaf’
Undefined global functions or variables:
  cdnaf empirical_density model1 model2 model3 model4 model5 model6
  model7 rnaf
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
add_gc_bias         13.208  0.033  13.267
create_read_numbers  7.688  0.244   8.419
* 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-3.9-bioc/meat/polyester.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL polyester
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘polyester’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (polyester)

name	user	system	elapsed
NB	0.000	0.000	0.001
add_error	0.131	0.012	0.148
add_gc_bias	13.208	0.033	13.267
add_platform_error	0.223	0.000	0.223
count_transcripts	0.022	0.000	0.021
create_read_numbers	7.688	0.244	8.419
fpkm_to_counts	0.070	0.000	0.069
generate_fragments	0.334	0.008	0.342
getAttributeField	1.087	0.072	1.172
get_params	0.047	0.004	0.051
get_reads	0.133	0.004	0.138
reverse_complement	0.124	0.002	0.126
seq_gtf	0	0	0
simulate_experiment	0	0	0
simulate_experiment_countmat	0.001	0.000	0.000
simulate_experiment_empirical	0	0	0
write_reads	0.113	0.004	0.118