BioC 3.5: CHECK report for polyester on tokay2

Package: polyester

Version: 1.12.0

Command: rm -rf polyester.buildbin-libdir polyester.Rcheck && mkdir polyester.buildbin-libdir polyester.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=polyester.buildbin-libdir polyester_1.12.0.tar.gz >polyester.Rcheck\00install.out 2>&1 && cp polyester.Rcheck\00install.out polyester-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=polyester.buildbin-libdir --install="check:polyester-install.out" --force-multiarch --no-vignettes --timings polyester_1.12.0.tar.gz

StartedAt: 2017-08-16 01:59:30 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:02:21 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 170.4 seconds

RetCode: 0

Status:  OK

CheckDir: polyester.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf polyester.buildbin-libdir polyester.Rcheck && mkdir polyester.buildbin-libdir polyester.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=polyester.buildbin-libdir polyester_1.12.0.tar.gz >polyester.Rcheck\00install.out 2>&1 && cp polyester.Rcheck\00install.out polyester-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=polyester.buildbin-libdir --install="check:polyester-install.out" --force-multiarch --no-vignettes --timings polyester_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/polyester.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'polyester/DESCRIPTION' ... OK
* this is package 'polyester' version '1.12.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
add_gc_bias         12.52   0.06   12.57
create_read_numbers  4.80   0.23    5.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
add_gc_bias         13.39   0.11   13.50
create_read_numbers  6.58   0.14    6.72
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/polyester.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'polyester' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'polyester' as polyester_1.12.0.zip
* DONE (polyester)

name	user	system	elapsed
NB	0	0	0
add_error	0.13	0.05	0.25
add_gc_bias	12.52	0.06	12.57
add_platform_error	0.45	0.04	0.49
count_transcripts	0.03	0.00	0.03
create_read_numbers	4.80	0.23	5.05
fpkm_to_counts	0.13	0.00	0.13
generate_fragments	0.84	0.04	0.94
getAttributeField	1.44	0.08	1.64
get_params	0.09	0.00	0.09
get_reads	0.19	0.02	0.21
reverse_complement	0.13	0.03	0.15
seq_gtf	0	0	0
simulate_experiment	0	0	0
simulate_experiment_countmat	0	0	0
simulate_experiment_empirical	0	0	0
write_reads	0.22	0.00	0.22

name	user	system	elapsed
NB	0	0	0
add_error	0.24	0.04	0.26
add_gc_bias	13.39	0.11	13.50
add_platform_error	0.66	0.03	0.69
count_transcripts	0.08	0.00	0.07
create_read_numbers	6.58	0.14	6.72
fpkm_to_counts	0.09	0.00	0.10
generate_fragments	1.05	0.06	1.12
getAttributeField	1.50	0.03	1.53
get_params	0.08	0.00	0.08
get_reads	0.17	0.00	0.17
reverse_complement	0.13	0.00	0.12
seq_gtf	0	0	0
simulate_experiment	0	0	0
simulate_experiment_countmat	0	0	0
simulate_experiment_empirical	0	0	0
write_reads	0.17	0.00	0.18