Package: QSutils

Version: 1.1.0

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_1.1.0.tar.gz

StartedAt: 2019-04-09 03:06:31 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:08:03 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 91.7 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/QSutils.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.1.0’
* 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’ ...
** 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
* DONE (QSutils)

name	user	system	elapsed
Collapse	0.144	0.009	0.155
ConsSeq	0.024	0.001	0.025
CorrectGapsAndNs	0.010	0.002	0.011
DBrule	0.058	0.007	0.068
DNA.dist	0.010	0.002	0.012
DSFT	0.007	0.001	0.007
Diverge	0.004	0.001	0.005
DottedAlignment	0.010	0.002	0.012
FAD	0.011	0.002	0.013
FreqMat	0.019	0.002	0.021
GenerateVars	0.004	0.001	0.004
GenotypeStandards_A-H.fas	0.006	0.000	0.006
GetInfProfile	0.029	0.004	0.034
GetQSData	0.472	0.057	0.532
GetRandomSeq	0.000	0.000	0.001
GiniSimpson	0.001	0.000	0.001
HCq	0.005	0.000	0.006
Hill	0.003	0.000	0.004
IntersectStrandHpls	0.126	0.003	0.133
MutationFreq	0.517	0.037	0.555
MutsTbl	0.016	0.002	0.018
NucleotideDiversity	0.006	0.000	0.007
PolyDist	0.026	0.001	0.026
Rao	0.012	0.001	0.012
ReadAmplSeqs	0.026	0.001	0.026
Renyi	0.003	0.000	0.005
ReportVariants	0.017	0.000	0.018
SegSites	0.012	0.001	0.013
Shannon	0.000	0.000	0.001
SortByMutations	0.520	0.061	0.583
SummaryMuts	0.018	0.001	0.019
TotalMutations	0.017	0.000	0.018
Toy.GapsAndNs.fna	0.066	0.004	0.071
ToyData_10_50_1000.fna	0.034	0.001	0.035
ToyData_FWReads.fna	0.098	0.005	0.102
ToyData_RVReads.fna	0.106	0.003	0.108
UniqueMutations	0.011	0.000	0.014
Unknown-Genotype.fna	0.010	0.001	0.012
fn.ab	0.006	0.001	0.006
geom.series	0.002	0.000	0.003