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BioC 3.4: CHECK report for polyester on zin1

This page was generated on 2016-09-21 03:39:19 -0700 (Wed, 21 Sep 2016).

Package 912/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
polyester 1.9.7
Jack Fu , Jeff Leek
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/polyester
Last Changed Rev: 120419 / Revision: 121152
Last Changed Date: 2016-08-24 20:53:29 -0700 (Wed, 24 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: polyester
Version: 1.9.7
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings polyester_1.9.7.tar.gz
StartedAt: 2016-09-20 10:40:54 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:42:22 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 87.1 seconds
RetCode: 0
Status:  OK 
CheckDir: polyester.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings polyester_1.9.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-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 ‘1.9.7’
* 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
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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
add_gc_bias 12.328  0.016  12.462
* 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-3.4-bioc/meat/polyester.Rcheck/00check.log’
for details.


polyester.Rcheck/00install.out:

* 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)

polyester.Rcheck/polyester-Ex.timings:

nameusersystemelapsed
NB000
add_error0.1080.0040.120
add_gc_bias12.328 0.01612.462
add_platform_error0.2240.0040.230
count_transcripts0.020.000.02
create_read_numbers4.2240.0884.339
fpkm_to_counts0.0480.0000.047
generate_fragments0.2520.0040.257
getAttributeField1.6240.0081.638
get_params0.0440.0040.048
get_reads0.1280.0000.129
reverse_complement0.1000.0200.122
seq_gtf0.0000.0000.001
simulate_experiment000
simulate_experiment_countmat000
simulate_experiment_empirical0.0000.0000.001
write_reads0.1360.0000.135