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 04:40:22 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:42:16 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 113.7 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) (2019-03-18 r76245)
* 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’ ...
** 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	0.182	0.023	0.207
ConsSeq	0.047	0.012	0.059
CorrectGapsAndNs	0.009	0.003	0.011
DBrule	0.085	0.018	0.107
DNA.dist	0.017	0.005	0.022
DSFT	0.009	0.003	0.012
Diverge	0.004	0.002	0.006
DottedAlignment	0.020	0.006	0.026
FAD	0.015	0.004	0.019
FreqMat	0.040	0.013	0.052
GenerateVars	0.009	0.003	0.012
GenotypeStandards_A-H.fas	0.012	0.003	0.015
GetInfProfile	0.029	0.008	0.038
GetQSData	0.592	0.092	0.685
GetRandomSeq	0.001	0.000	0.000
GiniSimpson	0.001	0.001	0.002
HCq	0.010	0.002	0.011
Hill	0.008	0.001	0.010
IntersectStrandHpls	0.139	0.012	0.156
MutationFreq	0.717	0.103	0.820
MutsTbl	0.034	0.005	0.040
NucleotideDiversity	0.013	0.001	0.014
PolyDist	0.053	0.002	0.054
Rao	0.022	0.002	0.023
ReadAmplSeqs	0.054	0.006	0.060
Renyi	0.007	0.003	0.010
ReportVariants	0.035	0.008	0.043
SegSites	0.016	0.001	0.017
Shannon	0.001	0.001	0.002
SortByMutations	0.688	0.101	0.789
SummaryMuts	0.020	0.001	0.021
TotalMutations	0.018	0.001	0.019
Toy.GapsAndNs.fna	0.060	0.004	0.063
ToyData_10_50_1000.fna	0.031	0.002	0.033
ToyData_FWReads.fna	0.087	0.006	0.094
ToyData_RVReads.fna	0.101	0.007	0.108
UniqueMutations	0.023	0.003	0.026
Unknown-Genotype.fna	0.018	0.001	0.019
fn.ab	0.007	0.002	0.009
geom.series	0.005	0.000	0.006