Package: QSutils

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2020-04-15 04:53:43 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:55:16 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 92.3 seconds

RetCode: 0

Status:  OK

CheckDir: QSutils.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/QSutils.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.0’
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL QSutils
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

name	user	system	elapsed
Collapse	0.168	0.012	0.183
ConsSeq	0.031	0.004	0.034
CorrectGapsAndNs	0.007	0.002	0.008
DBrule	0.072	0.005	0.079
DNA.dist	0.013	0.002	0.015
DSFT	0.006	0.000	0.006
Diverge	0.003	0.000	0.004
DottedAlignment	0.015	0.002	0.017
FAD	0.011	0.002	0.013
FreqMat	0.024	0.005	0.030
GenerateVars	0.007	0.001	0.008
GenotypeStandards_A-H.fas	0.011	0.001	0.012
GetInfProfile	0.035	0.006	0.042
GetQSData	0.700	0.075	0.777
GetRandomSeq	0.001	0.000	0.000
GiniSimpson	0.001	0.000	0.001
HCq	0.005	0.001	0.005
Hill	0.004	0.000	0.004
IntersectStrandHpls	0.122	0.003	0.131
MutationFreq	0.496	0.046	0.545
MutsTbl	0.018	0.002	0.019
NucleotideDiversity	0.007	0.000	0.007
PolyDist	0.027	0.000	0.027
Rao	0.013	0.001	0.014
ReadAmplSeqs	0.033	0.002	0.034
Renyi	0.004	0.001	0.005
ReportVariants	0.028	0.003	0.032
SegSites	0.017	0.000	0.018
Shannon	0.001	0.001	0.001
SortByMutations	0.563	0.031	0.597
SummaryMuts	0.024	0.001	0.025
TotalMutations	0.025	0.000	0.026
Toy.GapsAndNs.fna	0.075	0.002	0.078
ToyData_10_50_1000.fna	0.037	0.001	0.038
ToyData_FWReads.fna	0.104	0.002	0.107
ToyData_RVReads.fna	0.114	0.005	0.121
UniqueMutations	0.017	0.002	0.018
Unknown-Genotype.fna	0.016	0.001	0.016
fn.ab	0.005	0.001	0.006
geom.series	0.004	0.001	0.004