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BioC 3.5: CHECK report for MAST on malbec2

This page was generated on 2017-10-18 14:18:07 -0400 (Wed, 18 Oct 2017).

Package 758/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAST 1.2.1
Andrew McDavid
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/MAST
Branch: RELEASE_3_5
Last Commit: 4982bbd
Last Changed Date: 2017-09-01 01:10:45 -0400 (Fri, 01 Sep 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MAST
Version: 1.2.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MAST_1.2.1.tar.gz
StartedAt: 2017-10-18 00:32:17 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 00:35:39 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 202.2 seconds
RetCode: 0
Status:  OK 
CheckDir: MAST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MAST_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/MAST.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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  6.5Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    doc    1.9Mb
* 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 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/MAST.Rcheck/00check.log’
for details.


MAST.Rcheck/00install.out:

* 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)

MAST.Rcheck/MAST-Ex.timings:

nameusersystemelapsed
Drop0.0000.0000.001
FromFlatDF1.4520.0321.274
FromMatrix0.1240.0120.137
Hypothesis0.0080.0000.007
LRT0.2920.0000.292
ZlmFit-class1.5640.0001.565
applyFlat0.0040.0000.002
bootVcov10.3000.0000.298
cData0.0120.0000.013
calcZ1.2320.0041.197
collectResiduals1.2560.0001.186
computeEtFromCt0.0360.0160.052
convertMASTClassicToSingleCellAssay0.0080.0000.011
defaultPrior000
expavg000
filter0.4920.0080.500
filterLowExpressedGenes0.0160.0000.016
freq0.020.000.02
getConcordance0.2200.0000.221
getwellKey0.0080.0040.011
gseaAfterBoot0.8640.0040.844
hushWarning0.0080.0000.002
impute2.3240.0002.309
invlogit0.0040.0000.001
logFC0.2120.0000.204
logmean0.0000.0000.002
lrTest0.5200.0040.522
melt.SingleCellAssay0.0280.0040.030
plot.thresholdSCRNACountMatrix1.0520.0721.124
plotSCAConcordance0.6640.0080.673
predict.ZlmFit2.1280.0122.119
se.coef0.6600.0000.656
split-SingleCellAssay-character-method0.0600.0000.059
stat_ell1.3000.0041.281
subset-SingleCellAssay-method0.0240.0000.015
summary-GSEATests-method0.6800.0040.646
summary-ZlmFit-method0.3040.0040.197
thresholdSCRNACountMatrix0.4040.0560.462
waldTest0.4680.0080.476
zlm0.1600.0000.162