BioC 3.5: CHECK report for MAST on oaxaca

Package: MAST

Version: 1.1.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAST_1.1.6.tar.gz

StartedAt: 2017-03-04 05:15:54 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 05:20:02 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 248.2 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_1.1.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MAST.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.6’
* 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 loading without being on the library search path ... 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-3.5-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	0	0
FromFlatDF	0.846	0.036	0.882
FromMatrix	0.172	0.015	0.187
Hypothesis	0.010	0.000	0.011
LRT	0.349	0.014	0.363
ZlmFit-class	1.885	0.038	1.924
applyFlat	0.003	0.000	0.002
bootVcov1	0.387	0.014	0.401
cData	0.015	0.001	0.016
calcZ	1.012	0.019	1.031
collectResiduals	1.730	0.024	1.756
computeEtFromCt	0.051	0.007	0.058
convertMASTClassicToSingleCellAssay	0.012	0.002	0.015
defaultPrior	0.001	0.000	0.001
expavg	0.001	0.000	0.001
filter	0.673	0.010	0.683
filterLowExpressedGenes	0.018	0.002	0.019
freq	0.028	0.003	0.032
getConcordance	0.315	0.012	0.328
getwellKey	0.015	0.004	0.019
gseaAfterBoot	1.222	0.026	1.249
hushWarning	0.000	0.000	0.001
impute	3.579	0.016	3.599
invlogit	0.001	0.000	0.001
logFC	0.267	0.006	0.274
logmean	0.002	0.000	0.001
lrTest	0.757	0.006	0.763
melt.SingleCellAssay	0.039	0.002	0.042
plot.thresholdSCRNACountMatrix	1.295	0.030	1.328
plotSCAConcordance	0.850	0.026	0.877
predict.ZlmFit	2.911	0.017	2.929
se.coef	0.776	0.041	0.819
split-SingleCellAssay-character-method	0.055	0.001	0.057
stat_ell	1.824	0.011	1.837
subset-SingleCellAssay-method	0.023	0.002	0.024
summary-GSEATests-method	1.086	0.023	1.109
summary-ZlmFit-method	0.171	0.006	0.178
thresholdSCRNACountMatrix	0.421	0.030	0.453
waldTest	0.666	0.016	0.683
zlm	0.179	0.005	0.184