BioC 3.5: CHECK report for MAST on veracruz2

Package: MAST

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAST_1.2.1.tar.gz

StartedAt: 2017-10-18 05:38:17 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:42:33 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 256.8 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_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MAST.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.1’
* 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-3.5-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	0.001	0.000	0.001
FromFlatDF	1.419	0.099	1.352
FromMatrix	0.195	0.019	0.232
Hypothesis	0.009	0.001	0.010
LRT	0.406	0.015	0.432
ZlmFit-class	2.206	0.039	2.401
applyFlat	0.002	0.000	0.002
bootVcov1	0.394	0.008	0.417
cData	0.017	0.001	0.019
calcZ	1.110	0.019	1.146
collectResiduals	2.476	0.215	1.872
computeEtFromCt	0.049	0.008	0.059
convertMASTClassicToSingleCellAssay	0.013	0.002	0.015
defaultPrior	0.001	0.001	0.002
expavg	0.000	0.000	0.001
filter	0.690	0.015	0.762
filterLowExpressedGenes	0.025	0.002	0.029
freq	0.015	0.002	0.017
getConcordance	0.248	0.009	0.261
getwellKey	0.015	0.004	0.019
gseaAfterBoot	0.997	0.013	1.032
hushWarning	0.003	0.000	0.002
impute	3.279	0.044	3.377
invlogit	0.000	0.001	0.001
logFC	0.282	0.009	0.308
logmean	0.001	0.000	0.002
lrTest	0.669	0.018	0.697
melt.SingleCellAssay	0.040	0.003	0.045
plot.thresholdSCRNACountMatrix	1.145	0.037	1.213
plotSCAConcordance	0.867	0.025	0.924
predict.ZlmFit	2.915	0.017	3.018
se.coef	0.617	0.023	0.637
split-SingleCellAssay-character-method	0.051	0.002	0.053
stat_ell	1.697	0.015	1.766
subset-SingleCellAssay-method	0.020	0.002	0.019
summary-GSEATests-method	0.880	0.023	0.914
summary-ZlmFit-method	0.195	0.012	0.194
thresholdSCRNACountMatrix	0.502	0.036	0.558
waldTest	0.624	0.023	0.658
zlm	0.201	0.004	0.208