Package: QSutils

Version: 1.2.0

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_1.2.0.tar.gz

StartedAt: 2019-10-16 05:54:31 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:56:35 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 124.0 seconds

RetCode: 0

Status:  OK

CheckDir: QSutils.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/QSutils.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.0’
* 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

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


* 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	0.233	0.031	0.266
ConsSeq	0.035	0.005	0.041
CorrectGapsAndNs	0.011	0.003	0.013
DBrule	0.086	0.013	0.103
DNA.dist	0.014	0.002	0.016
DSFT	0.009	0.002	0.010
Diverge	0.005	0.002	0.006
DottedAlignment	0.016	0.003	0.019
FAD	0.009	0.001	0.009
FreqMat	0.040	0.012	0.052
GenerateVars	0.009	0.002	0.012
GenotypeStandards_A-H.fas	0.014	0.003	0.017
GetInfProfile	0.038	0.009	0.047
GetQSData	0.628	0.115	0.743
GetRandomSeq	0.000	0.000	0.001
GiniSimpson	0.001	0.001	0.001
HCq	0.005	0.001	0.007
Hill	0.005	0.001	0.005
IntersectStrandHpls	0.155	0.011	0.169
MutationFreq	0.672	0.088	0.760
MutsTbl	0.038	0.005	0.044
NucleotideDiversity	0.013	0.001	0.014
PolyDist	0.054	0.001	0.055
Rao	0.024	0.002	0.026
ReadAmplSeqs	0.039	0.002	0.040
Renyi	0.008	0.002	0.009
ReportVariants	0.027	0.003	0.031
SegSites	0.018	0.002	0.021
Shannon	0.001	0.001	0.003
SortByMutations	0.659	0.085	0.745
SummaryMuts	0.020	0.001	0.021
TotalMutations	0.024	0.001	0.025
Toy.GapsAndNs.fna	0.080	0.006	0.086
ToyData_10_50_1000.fna	0.041	0.007	0.048
ToyData_FWReads.fna	0.144	0.011	0.156
ToyData_RVReads.fna	0.114	0.011	0.125
UniqueMutations	0.020	0.000	0.022
Unknown-Genotype.fna	0.021	0.004	0.025
fn.ab	0.007	0.002	0.008
geom.series	0.005	0.000	0.005