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BioC 3.5: CHECK report for MAST on veracruz2

This page was generated on 2017-08-16 13:35:07 -0400 (Wed, 16 Aug 2017).

Package 758/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAST 1.2.1
Andrew McDavid
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MAST
Last Changed Rev: 129473 / Revision: 131943
Last Changed Date: 2017-05-08 16:23:30 -0400 (Mon, 08 May 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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAST_1.2.1.tar.gz
StartedAt: 2017-08-16 04:52:11 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 04:56:55 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 283.6 seconds
RetCode: 0
Status:  OK 
CheckDir: MAST.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘1.2.1’
* 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.


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
Drop0.0010.0000.001
FromFlatDF2.0070.4521.113
FromMatrix0.1220.0150.137
Hypothesis0.0070.0000.008
LRT0.3020.0110.327
ZlmFit-class1.8950.0311.983
applyFlat0.0010.0000.002
bootVcov10.3740.0050.392
cData0.0120.0010.013
calcZ1.1050.0191.124
collectResiduals2.3960.3161.589
computeEtFromCt0.3950.0110.422
convertMASTClassicToSingleCellAssay0.0110.0020.014
defaultPrior0.0010.0000.001
expavg0.0010.0000.001
filter0.6620.0090.682
filterLowExpressedGenes0.0140.0020.015
freq0.0180.0030.023
getConcordance0.1940.0070.210
getwellKey0.0160.0050.021
gseaAfterBoot1.0770.0141.111
hushWarning0.0030.0010.001
impute3.0280.0582.976
invlogit0.0010.0000.000
logFC0.4310.0600.263
logmean0.0030.0010.001
lrTest0.8520.0560.748
melt.SingleCellAssay0.0380.0020.040
plot.thresholdSCRNACountMatrix1.3820.0351.455
plotSCAConcordance0.7790.0240.841
predict.ZlmFit2.3400.0332.443
se.coef1.1980.0721.106
split-SingleCellAssay-character-method0.0480.0020.050
stat_ell1.4660.0101.536
subset-SingleCellAssay-method0.0310.0060.019
summary-GSEATests-method1.0420.0610.950
summary-ZlmFit-method0.3310.0530.192
thresholdSCRNACountMatrix0.5510.0770.471
waldTest0.6630.0100.698
zlm0.2180.0020.225