Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:48 -0400 (Fri, 15 Oct 2021).

CHECK results for polyester on nebbiolo1

To the developers/maintainers of the polyester package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/polyester.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1412/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
polyester 1.28.0  (landing page)
Jack Fu , Jeff Leek
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/polyester
git_branch: RELEASE_3_13
git_last_commit: a71cce4
git_last_commit_date: 2021-05-19 12:08:02 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: polyester
Version: 1.28.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:polyester.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings polyester_1.28.0.tar.gz
StartedAt: 2021-10-14 11:04:02 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:05:55 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 112.7 seconds
RetCode: 0
Status:   OK  
CheckDir: polyester.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:polyester.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings polyester_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/polyester.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.28.0’
* 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’
simulate_experiment_countmat: no visible global function definition for
  ‘is’
Undefined global functions or variables:
  cdnaf empirical_density is model1 model2 model3 model4 model5 model6
  model7 rnaf
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 (user + system) or elapsed time > 5s
                      user system elapsed
add_gc_bias         13.679  0.095  13.778
create_read_numbers 10.095  0.787  10.886
* 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-3.13-bioc/meat/polyester.Rcheck/00check.log’
for details.



Installation output

polyester.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL polyester
###
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* installing to library ‘/home/biocbuild/bbs-3.13-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)

Tests output


Example timings

polyester.Rcheck/polyester-Ex.timings

nameusersystemelapsed
NB0.0010.0000.000
add_error0.1100.0270.138
add_gc_bias13.679 0.09513.778
add_platform_error0.2590.0010.259
count_transcripts0.0270.0030.031
create_read_numbers10.095 0.78710.886
fpkm_to_counts1.4770.0041.482
generate_fragments0.2770.0160.293
getAttributeField0.6340.0320.667
get_params1.5290.0041.533
get_reads0.2010.0080.209
reverse_complement0.1740.0000.175
seq_gtf000
simulate_experiment000
simulate_experiment_countmat000
simulate_experiment_empirical0.0000.0000.001
write_reads0.1560.0080.165