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CHECK report for QSutils on malbec2

This page was generated on 2021-01-17 12:32:31 -0500 (Sun, 17 Jan 2021).

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 1395/1931HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QSutils 1.9.0
Mercedes Guerrero-Murillo
Snapshot Date: 2021-01-16 14:40:27 -0500 (Sat, 16 Jan 2021)
URL: https://git.bioconductor.org/packages/QSutils
Branch: master
Last Commit: a1e3237
Last Changed Date: 2020-10-27 11:39:52 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 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
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: QSutils
Version: 1.9.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:QSutils.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings QSutils_1.9.0.tar.gz
StartedAt: 2021-01-17 04:40:54 -0500 (Sun, 17 Jan 2021)
EndedAt: 2021-01-17 04:42:22 -0500 (Sun, 17 Jan 2021)
EllapsedTime: 87.9 seconds
RetCode: 0
Status:  OK 
CheckDir: QSutils.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:QSutils.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings QSutils_1.9.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/QSutils.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* 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 ‘1.9.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/QSutils.Rcheck/00check.log’
for details.



Installation output

QSutils.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL QSutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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
Collapse0.4480.0040.458
ConsSeq0.0360.0000.036
CorrectGapsAndNs0.0090.0000.010
DBrule0.0760.0040.088
DNA.dist0.0080.0040.013
DSFT0.0080.0000.009
Diverge0.0040.0000.004
DottedAlignment0.0140.0000.014
FAD0.0090.0020.011
FreqMat0.0200.0090.028
GenerateVars0.0040.0000.005
GenotypeStandards_A-H.fas0.010.000.01
GetInfProfile0.0280.0040.031
GetQSData0.7980.0440.843
GetRandomSeq000
GiniSimpson0.0010.0000.000
HCq0.0070.0000.006
Hill0.0050.0000.005
IntersectStrandHpls0.1170.0000.118
MutationFreq0.6610.0320.693
MutsTbl0.0270.0000.028
NucleotideDiversity0.0110.0000.011
PolyDist0.0430.0000.043
Rao0.0180.0000.019
ReadAmplSeqs0.0410.0000.041
Renyi0.0060.0000.006
ReportVariants0.0270.0000.026
SegSites0.0120.0040.016
Shannon0.0010.0000.001
SortByMutations0.4780.0000.478
SummaryMuts0.0120.0040.015
TotalMutations0.0140.0000.014
Toy.GapsAndNs.fna0.0510.0000.051
ToyData_10_50_1000.fna0.0420.0000.042
ToyData_FWReads.fna0.1150.0000.115
ToyData_RVReads.fna0.1040.0080.111
UniqueMutations0.0140.0000.014
Unknown-Genotype.fna0.010.000.01
fn.ab0.0040.0000.003
geom.series0.0030.0000.003