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CHECK report for MAST on malbec1

This page was generated on 2019-04-16 11:52:23 -0400 (Tue, 16 Apr 2019).

Package 885/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAST 1.8.2
Andrew McDavid
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/MAST
Branch: RELEASE_3_8
Last Commit: 7ae6306
Last Changed Date: 2019-01-16 08:49:30 -0400 (Wed, 16 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MAST
Version: 1.8.2
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MAST.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MAST_1.8.2.tar.gz
StartedAt: 2019-04-16 01:08:39 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:13:20 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 280.6 seconds
RetCode: 0
Status:  OK 
CheckDir: MAST.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MAST.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MAST_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/MAST.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.2’
* 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  5.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
collectResiduals      21.716  0.052   5.165
LRT                    7.924  0.016   1.495
summary-ZlmFit-method  7.272  0.012   1.263
FromFlatDF             6.260  0.032   1.941
* 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-3.8-bioc/meat/MAST.Rcheck/00check.log’
for details.



Installation output

MAST.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL MAST
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘MAST’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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: SingleCellExperiment
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, 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: 279 SKIPPED: 5 FAILED: 0
> 
> proc.time()
   user  system elapsed 
112.272   0.892  64.988 

Example timings

MAST.Rcheck/MAST-Ex.timings

nameusersystemelapsed
Drop0.0000.0000.001
FromFlatDF6.2600.0321.941
FromMatrix0.2080.0040.213
Hypothesis0.0080.0040.011
LRT7.9240.0161.495
ZlmFit-class1.6400.0041.224
applyFlat0.0000.0000.002
bootVcov10.9200.0000.633
cData0.040.000.04
calcZ4.2000.0121.420
collectResiduals21.716 0.052 5.165
computeEtFromCt0.0720.0080.078
convertMASTClassicToSingleCellAssay0.0240.0000.023
defaultAssay0.0560.0000.053
defaultPrior0.0000.0000.001
expavg0.0040.0000.001
filterLowExpressedGenes0.0520.0040.055
freq0.0360.0000.037
getConcordance0.6720.0040.287
getwellKey0.0200.0040.022
gseaAfterBoot4.1600.0241.431
hushWarning0.0040.0000.002
impute3.0120.0601.919
invlogit0.0000.0000.001
logFC2.6240.0080.568
logmean0.0000.0000.001
lrTest1.3600.0081.076
mast_filter0.4760.0000.475
melt.SingleCellAssay1.5080.0000.261
plot.thresholdSCRNACountMatrix0.5000.0120.515
plotSCAConcordance1.5800.0080.823
predict.ZlmFit2.9280.0161.709
se.coef1.2480.0080.944
split-SingleCellAssay-character-method0.0960.0000.098
stat_ell3.0280.0081.962
subset-SingleCellAssay-method0.0320.0000.032
summary-GSEATests-method4.5640.0121.732
summary-ZlmFit-method7.2720.0121.263
thresholdSCRNACountMatrix0.5400.0160.560
waldTest1.2160.0040.902
zlm0.8440.0000.400