BioC 3.6: CHECK report for MAST on veracruz1

Package: MAST

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAST_1.3.1.tar.gz

StartedAt: 2017-08-16 05:10:17 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:14:52 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 275.0 seconds

RetCode: 0

Status:  OK

CheckDir: MAST.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAST_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MAST.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAST’ version ‘1.3.1’
* 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 ‘MAST’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    doc    2.6Mb
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/MAST.Rcheck/00check.log’
for details.

* installing *source* package ‘MAST’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MAST)

name	user	system	elapsed
Drop	0.001	0.001	0.001
FromFlatDF	1.457	0.177	1.150
FromMatrix	0.184	0.016	0.202
Hypothesis	0.010	0.000	0.009
LRT	0.339	0.013	0.362
ZlmFit-class	2.043	0.029	2.118
applyFlat	0.002	0.000	0.002
bootVcov1	0.425	0.006	0.442
cData	0.014	0.001	0.015
calcZ	1.497	0.017	1.522
collectResiduals	2.215	0.228	1.661
computeEtFromCt	0.037	0.005	0.041
convertMASTClassicToSingleCellAssay	0.011	0.002	0.012
defaultPrior	0	0	0
expavg	0.001	0.000	0.001
filter	0.670	0.010	0.708
filterLowExpressedGenes	0.014	0.001	0.017
freq	0.012	0.002	0.015
getConcordance	0.269	0.010	0.283
getwellKey	0.016	0.005	0.021
gseaAfterBoot	1.116	0.015	1.160
hushWarning	0.002	0.000	0.001
impute	3.048	0.058	3.040
invlogit	0.002	0.001	0.001
logFC	0.530	0.118	0.269
logmean	0.002	0.001	0.001
lrTest	0.904	0.111	0.704
melt.SingleCellAssay	0.032	0.002	0.035
plot.thresholdSCRNACountMatrix	1.208	0.030	1.298
plotSCAConcordance	0.703	0.019	0.738
predict.ZlmFit	2.259	0.017	2.372
se.coef	0.911	0.148	0.706
split-SingleCellAssay-character-method	0.046	0.002	0.051
stat_ell	1.898	0.019	1.957
subset-SingleCellAssay-method	0.031	0.006	0.020
summary-GSEATests-method	0.981	0.059	0.876
summary-ZlmFit-method	0.369	0.061	0.208
thresholdSCRNACountMatrix	0.530	0.067	0.427
waldTest	0.694	0.014	0.750
zlm	0.214	0.003	0.228