Package: QSutils

Version: 1.5.0

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_1.5.0.tar.gz

StartedAt: 2020-01-16 07:51:36 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:53:43 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 127.3 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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/QSutils.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.5.0’
* 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/4.0/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	0.226	0.016	0.244
ConsSeq	0.055	0.010	0.065
CorrectGapsAndNs	0.014	0.004	0.018
DBrule	0.079	0.016	0.099
DNA.dist	0.018	0.005	0.023
DSFT	0.010	0.003	0.013
Diverge	0.006	0.002	0.008
DottedAlignment	0.019	0.004	0.023
FAD	0.016	0.004	0.020
FreqMat	0.048	0.016	0.063
GenerateVars	0.008	0.002	0.010
GenotypeStandards_A-H.fas	0.016	0.003	0.019
GetInfProfile	0.046	0.012	0.059
GetQSData	0.834	0.144	0.979
GetRandomSeq	0	0	0
GiniSimpson	0.001	0.002	0.002
HCq	0.006	0.001	0.006
Hill	0.004	0.001	0.005
IntersectStrandHpls	0.153	0.006	0.161
MutationFreq	0.735	0.102	0.837
MutsTbl	0.039	0.007	0.046
NucleotideDiversity	0.014	0.001	0.015
PolyDist	0.054	0.001	0.055
Rao	0.024	0.002	0.026
ReadAmplSeqs	0.061	0.003	0.063
Renyi	0.006	0.001	0.008
ReportVariants	0.034	0.003	0.038
SegSites	0.021	0.001	0.021
Shannon	0.001	0.001	0.002
SortByMutations	0.766	0.045	0.812
SummaryMuts	0.034	0.001	0.035
TotalMutations	0.029	0.001	0.029
Toy.GapsAndNs.fna	0.096	0.005	0.101
ToyData_10_50_1000.fna	0.041	0.001	0.043
ToyData_FWReads.fna	0.140	0.006	0.145
ToyData_RVReads.fna	0.154	0.012	0.165
UniqueMutations	0.020	0.001	0.021
Unknown-Genotype.fna	0.021	0.005	0.025
fn.ab	0.005	0.002	0.007
geom.series	0.004	0.001	0.005