Package: QSutils

Version: 1.1.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:QSutils.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings QSutils_1.1.0.tar.gz

StartedAt: 2019-04-09 02:55:57 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:57:22 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 85.2 seconds

RetCode: 0

Status:  OK

CheckDir: QSutils.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:QSutils.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings QSutils_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/QSutils.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL QSutils
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	0.106	0.004	0.123
ConsSeq	0.031	0.004	0.035
CorrectGapsAndNs	0.006	0.004	0.010
DBrule	0.067	0.008	0.075
DNA.dist	0.008	0.000	0.007
DSFT	0.002	0.004	0.006
Diverge	0.001	0.001	0.002
DottedAlignment	0.006	0.002	0.009
FAD	0.004	0.004	0.008
FreqMat	0.013	0.004	0.017
GenerateVars	0.003	0.000	0.003
GenotypeStandards_A-H.fas	0.007	0.000	0.006
GetInfProfile	0.016	0.004	0.020
GetQSData	0.416	0.012	0.429
GetRandomSeq	0	0	0
GiniSimpson	0.001	0.000	0.001
HCq	0.003	0.004	0.008
Hill	0.006	0.000	0.006
IntersectStrandHpls	0.116	0.000	0.152
MutationFreq	0.536	0.011	0.552
MutsTbl	0.011	0.003	0.015
NucleotideDiversity	0.007	0.001	0.007
PolyDist	0.024	0.000	0.024
Rao	0.013	0.000	0.013
ReadAmplSeqs	0.023	0.000	0.023
Renyi	0.000	0.002	0.003
ReportVariants	0.014	0.001	0.014
SegSites	0.009	0.000	0.009
Shannon	0.001	0.000	0.001
SortByMutations	0.417	0.008	0.424
SummaryMuts	0.014	0.000	0.014
TotalMutations	0.013	0.000	0.013
Toy.GapsAndNs.fna	0.041	0.000	0.041
ToyData_10_50_1000.fna	0.023	0.000	0.023
ToyData_FWReads.fna	0.055	0.004	0.060
ToyData_RVReads.fna	0.058	0.000	0.058
UniqueMutations	0.008	0.000	0.008
Unknown-Genotype.fna	0.007	0.000	0.007
fn.ab	0.003	0.000	0.003
geom.series	0.002	0.000	0.002