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CHECK report for polyester on merida2

This page was generated on 2018-10-17 08:53:39 -0400 (Wed, 17 Oct 2018).

Package 1112/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
polyester 1.16.0
Jack Fu , Jeff Leek
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/polyester
Branch: RELEASE_3_7
Last Commit: 1a14fff
Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: polyester
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:polyester.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings polyester_1.16.0.tar.gz
StartedAt: 2018-10-16 23:18:09 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:20:06 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 117.1 seconds
RetCode: 0
Status:  OK 
CheckDir: polyester.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:polyester.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings polyester_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/polyester.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘polyester/DESCRIPTION’ ... OK
* this is package ‘polyester’ version ‘1.16.0’
* 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         12.730  0.130  12.930
create_read_numbers  7.689  0.282   8.076
* 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/polyester.Rcheck/00check.log’
for details.



Installation output

polyester.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL polyester
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘polyester’ ...
** 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
* DONE (polyester)

Tests output


Example timings

polyester.Rcheck/polyester-Ex.timings

nameusersystemelapsed
NB0.0020.0010.002
add_error0.1520.0190.173
add_gc_bias12.73 0.1312.93
add_platform_error0.3320.0260.364
count_transcripts0.0310.0090.039
create_read_numbers7.6890.2828.076
fpkm_to_counts0.0650.0040.069
generate_fragments0.2910.0150.317
getAttributeField1.6900.1611.859
get_params0.0630.0050.070
get_reads0.1550.0060.163
reverse_complement0.1490.0060.156
seq_gtf0.0020.0000.002
simulate_experiment0.0000.0000.001
simulate_experiment_countmat0.0010.0000.001
simulate_experiment_empirical0.0020.0010.003
write_reads0.1480.0090.161