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CHECK report for SynExtend on nebbiolo1

This page was generated on 2021-01-19 11:54:31 -0500 (Tue, 19 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE SynExtend PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1829/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SynExtend 1.2.0
Nicholas Cooley
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/SynExtend
Branch: RELEASE_3_12
Last Commit: 5786318
Last Changed Date: 2020-10-27 11:56:55 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SynExtend
Version: 1.2.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings SynExtend_1.2.0.tar.gz
StartedAt: 2021-01-18 23:20:47 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 23:25:00 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 252.9 seconds
RetCode: 0
Status:  OK 
CheckDir: SynExtend.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings SynExtend_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/SynExtend.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘SynExtend’ 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
Package in Depends field not imported from: ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PairSummaries: no visible binding for global variable ‘GlobalSelect’
PairSummaries: no visible binding for global variable ‘LocalSelect’
PairSummaries: no visible binding for global variable ‘ExactSelect’
Undefined global functions or variables:
  ExactSelect GlobalSelect LocalSelect
* 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
NucleotideOverlap 77.922  0.464  78.517
PairSummaries     76.900  0.124  77.070
gffToDataFrame    19.246  0.004  19.251
* 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-3.12-bioc/meat/SynExtend.Rcheck/00check.log’
for details.



Installation output

SynExtend.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL SynExtend
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘SynExtend’ ...
** 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 (SynExtend)

Tests output


Example timings

SynExtend.Rcheck/SynExtend-Ex.timings

nameusersystemelapsed
ExactSelect0.0030.0000.004
GlobalSelect0.0000.0020.002
LocalSelect0.0010.0000.002
NucleotideOverlap77.922 0.46478.517
PairSummaries76.900 0.12477.070
gffToDataFrame19.246 0.00419.251