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BioC 3.4: CHECK report for MAST on malbec1

This page was generated on 2017-04-15 16:14:09 -0400 (Sat, 15 Apr 2017).

Package 714/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAST 1.0.5
Andrew McDavid
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/MAST
Last Changed Rev: 124349 / Revision: 128728
Last Changed Date: 2016-11-22 11:37:49 -0500 (Tue, 22 Nov 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MAST
Version: 1.0.5
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MAST_1.0.5.tar.gz
StartedAt: 2017-04-14 23:37:59 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:41:08 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 189.3 seconds
RetCode: 0
Status:  OK 
CheckDir: MAST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MAST_1.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MAST.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.5’
* 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  6.4Mb
  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 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 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-3.4-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
Drop000
FromFlatDF1.1280.0120.952
FromMatrix0.0200.0040.023
Hypothesis0.0120.0000.012
LRT0.1520.0000.153
ZlmFit-class0.6840.0040.688
applyFlat0.0000.0000.002
bootVcov10.3240.0000.322
cData0.0120.0000.013
calcZ0.8600.0000.825
collectResiduals1.6280.0041.564
computeEtFromCt0.0320.0000.034
condmean0.0120.0000.012
convertMASTClassicToSingleCellAssay0.0120.0000.009
defaultPrior0.0000.0000.001
expavg000
filter0.3720.0000.373
filterLowExpressedGenes0.0160.0000.016
freq0.0120.0000.010
getConcordance0.0840.0000.084
getwellKey0.0080.0000.012
gseaAfterBoot0.8640.0000.835
hushWarning0.0080.0000.002
impute1.3840.0001.358
invlogit0.0000.0000.001
logFC0.1760.0080.174
logmean0.0000.0000.001
lrTest0.5560.0080.566
melt.SingleCellAssay0.0280.0000.026
plot.thresholdSCRNACountMatrix0.9800.0120.994
plotSCAConcordance0.3000.0080.311
predict.ZlmFit1.5600.0321.574
se.coef0.6240.0000.626
split-SingleCellAssay-character-method0.0480.0000.051
stat_ell1.4480.0041.423
subset-SingleCellAssay-method0.0240.0000.020
summary-GSEATests-method1.1520.0041.115
summary-ZlmFit-method0.2720.0040.168
thresholdSCRNACountMatrix0.2800.0080.291
waldTest0.5400.0000.542
zlm0.0440.0000.044
zlm.SingleCellAssay0.1880.0000.188