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CHECK report for QSutils on malbec2

This page was generated on 2020-10-17 11:55:28 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE QSutils PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1395/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QSutils 1.6.0
Mercedes Guerrero-Murillo
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/QSutils
Branch: RELEASE_3_11
Last Commit: 22b04ea
Last Changed Date: 2020-04-27 15:20:49 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: QSutils
Version: 1.6.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:QSutils.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings QSutils_1.6.0.tar.gz
StartedAt: 2020-10-17 04:27:03 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:28:25 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 82.4 seconds
RetCode: 0
Status:  OK 
CheckDir: QSutils.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:QSutils.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings QSutils_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/QSutils.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 ‘QSutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QSutils’ version ‘1.6.0’
* 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 ‘QSutils’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: OK


Installation output

QSutils.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL QSutils
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘QSutils’ ...
** using staged installation
** R
** 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 (QSutils)

Tests output


Example timings

QSutils.Rcheck/QSutils-Ex.timings

nameusersystemelapsed
Collapse0.1110.0000.119
ConsSeq0.0220.0000.022
CorrectGapsAndNs0.0070.0000.006
DBrule0.0420.0040.047
DNA.dist0.0080.0000.007
DSFT0.0020.0040.005
Diverge0.0020.0000.003
DottedAlignment0.0050.0040.009
FAD0.0070.0000.007
FreqMat0.0130.0040.017
GenerateVars0.0040.0000.003
GenotypeStandards_A-H.fas0.0060.0000.006
GetInfProfile0.0180.0000.018
GetQSData0.650.040.69
GetRandomSeq0.0010.0000.000
GiniSimpson0.0010.0000.000
HCq0.0020.0030.004
Hill0.0020.0000.003
IntersectStrandHpls0.0680.0000.070
MutationFreq0.4520.0120.464
MutsTbl0.0150.0000.015
NucleotideDiversity0.0060.0000.006
PolyDist0.0220.0000.022
Rao0.0120.0000.012
ReadAmplSeqs0.0250.0000.025
Renyi0.0030.0000.004
ReportVariants0.0160.0000.016
SegSites0.010.000.01
Shannon0.0010.0000.001
SortByMutations0.4610.0000.461
SummaryMuts0.0160.0000.016
TotalMutations0.0150.0000.015
Toy.GapsAndNs.fna0.0460.0000.046
ToyData_10_50_1000.fna0.0280.0000.028
ToyData_FWReads.fna0.0570.0080.065
ToyData_RVReads.fna0.0620.0040.066
UniqueMutations0.0070.0040.011
Unknown-Genotype.fna0.0110.0000.010
fn.ab0.0030.0010.004
geom.series0.0000.0020.003