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CHECK report for QSutils on machv2

This page was generated on 2021-01-17 12:39:45 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:QSutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings QSutils_1.9.0.tar.gz
StartedAt: 2021-01-17 03:29:37 -0500 (Sun, 17 Jan 2021)
EndedAt: 2021-01-17 03:31:16 -0500 (Sun, 17 Jan 2021)
EllapsedTime: 99.1 seconds
RetCode: 0
Status:  OK 
CheckDir: QSutils.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:QSutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings QSutils_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/QSutils.Rcheck’
* using R Under development (unstable) (2021-01-06 r79800)
* using platform: x86_64-apple-darwin17.0 (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
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/QSutils.Rcheck/00check.log’
for details.



Installation output

QSutils.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL QSutils
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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
Collapse0.3430.0050.348
ConsSeq0.0240.0010.026
CorrectGapsAndNs0.0060.0020.007
DBrule0.0590.0060.065
DNA.dist0.0110.0020.014
DSFT0.0060.0010.007
Diverge0.0030.0000.004
DottedAlignment0.0090.0010.010
FAD0.0070.0010.008
FreqMat0.0190.0050.024
GenerateVars0.0040.0010.005
GenotypeStandards_A-H.fas0.0070.0010.008
GetInfProfile0.0220.0040.026
GetQSData0.5430.0370.580
GetRandomSeq000
GiniSimpson0.0010.0010.001
HCq0.0050.0010.006
Hill0.0040.0010.005
IntersectStrandHpls0.1210.0050.128
MutationFreq0.5950.0830.679
MutsTbl0.0180.0030.021
NucleotideDiversity0.0070.0000.008
PolyDist0.0320.0010.033
Rao0.0130.0010.014
ReadAmplSeqs0.0260.0010.028
Renyi0.0040.0000.004
ReportVariants0.0190.0010.020
SegSites0.0110.0010.011
Shannon0.0010.0010.001
SortByMutations0.5620.0260.589
SummaryMuts0.0290.0010.031
TotalMutations0.0210.0000.023
Toy.GapsAndNs.fna0.0760.0040.080
ToyData_10_50_1000.fna0.0410.0030.043
ToyData_FWReads.fna0.1290.0050.135
ToyData_RVReads.fna0.0930.0070.100
UniqueMutations0.0130.0010.014
Unknown-Genotype.fna0.0180.0020.020
fn.ab0.0040.0010.006
geom.series0.0050.0010.006