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CHECK report for MAST on malbec1

This page was generated on 2018-04-12 13:15:32 -0400 (Thu, 12 Apr 2018).

Package 790/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAST 1.4.1
Andrew McDavid
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/MAST
Branch: RELEASE_3_6
Last Commit: 3ed9981
Last Changed Date: 2017-12-22 11:18:42 -0400 (Fri, 22 Dec 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MAST
Version: 1.4.1
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MAST_1.4.1.tar.gz
StartedAt: 2018-04-12 00:47:57 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:51:17 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 199.4 seconds
RetCode: 0
Status:  OK 
CheckDir: MAST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MAST_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MAST.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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  8.2Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    doc    3.7Mb
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/MAST.Rcheck/00check.log’
for details.



Installation output

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)

Tests output

MAST.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("MAST")
Loading required package: MAST
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply


Attaching package: 'MAST'

The following object is masked from 'package:stats':

    filter

Error : number of levels of each grouping factor must be < number of observations
(0.0426,0.354]  (0.354,0.757]   (0.757,1.28]    (1.28,1.96]    (1.96,2.84] 
      2.258200       2.258200       2.258200       2.258200       2.258200 
   (2.84,3.99]    (3.99,13.2] 
      2.258200       3.313588 
(0.0602,0.436]   (0.436,0.67]   (0.67,0.944]   (0.944,1.26]    (1.26,1.63] 
      1.967142       1.967142       1.967142       2.003488       2.003488 
   (1.63,2.06]    (2.06,2.56]    (2.56,3.83] 
      2.600202       2.600202       2.600202 
    (0.03,1.56]     (1.56,5.36]     (5.36,14.8] (14.8,9.25e+03] 
       238.2279        238.2279        238.2279       4525.1912 
Error in (function (x, y, weights = rep(1, nobs), start = NULL, etastart = NULL,  : 
  NAs in V(mu)
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 277 SKIPPED: 5 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 33.276   0.384  44.777 

Example timings

MAST.Rcheck/MAST-Ex.timings

nameusersystemelapsed
Drop0.0000.0000.001
FromFlatDF1.3480.0201.142
FromMatrix0.1400.0000.141
Hypothesis0.0080.0000.006
LRT0.2800.0160.298
ZlmFit-class1.5160.0041.522
applyFlat0.0040.0000.002
bootVcov10.3040.0040.310
cData0.3160.0040.321
calcZ0.8760.0000.843
collectResiduals1.1520.0041.082
computeEtFromCt0.0320.0080.041
convertMASTClassicToSingleCellAssay0.0120.0000.010
defaultPrior0.0000.0000.001
expavg0.0000.0000.001
filterLowExpressedGenes0.020.000.02
freq0.0120.0040.015
getConcordance0.2120.0040.214
getwellKey0.0120.0000.012
gseaAfterBoot0.8120.0000.772
hushWarning0.0000.0000.002
impute2.5960.0202.614
invlogit0.0040.0000.001
logFC0.2000.0040.200
logmean0.0000.0000.001
lrTest0.5080.0040.513
mast_filter0.5520.0000.554
melt.SingleCellAssay0.0280.0000.031
plot.thresholdSCRNACountMatrix1.3080.0201.331
plotSCAConcordance0.7600.0000.761
predict.ZlmFit1.8880.0041.870
se.coef0.4440.0000.443
split-SingleCellAssay-character-method0.0360.0040.040
stat_ell1.7640.0001.749
subset-SingleCellAssay-method0.0200.0000.017
summary-GSEATests-method0.7160.0080.686
summary-ZlmFit-method0.2520.0040.173
thresholdSCRNACountMatrix0.7560.0200.777
waldTest0.7600.0080.769
zlm0.2280.0000.230