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CHECK report for MAST on machv2

This page was generated on 2020-10-17 11:58:51 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE MAST PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 994/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAST 1.14.0
Andrew McDavid
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MAST
Branch: RELEASE_3_11
Last Commit: b415934
Last Changed Date: 2020-04-27 15:02:36 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MAST
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MAST.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MAST_1.14.0.tar.gz
StartedAt: 2020-10-17 02:38:55 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:45:29 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 394.7 seconds
RetCode: 0
Status:  OK 
CheckDir: MAST.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MAST.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MAST_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/MAST.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.0’
* package encoding: UTF-8
* 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  5.0Mb
  sub-directories of 1Mb or more:
    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
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/MAST.Rcheck/00check.log’
for details.



Installation output

MAST.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MAST
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘MAST’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MAST)

Tests output

MAST.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, 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 objects are masked from 'package:base':

    aperm, apply, rowsum

Error : number of levels of each grouping factor must be < number of observations (problems: Subject.ID)
(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 : grouping factors must have > 1 sampled level
NULL
NULL
NULL
Error in (function (x, y, weights = rep.int(1, nobs), start = NULL, etastart = NULL,  : 
  NAs in V(mu)
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 287 | SKIPPED: 4 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 71.889   1.540  94.718 

Example timings

MAST.Rcheck/MAST-Ex.timings

nameusersystemelapsed
Drop0.0010.0010.001
FromFlatDF1.4620.0321.496
FromMatrix0.2410.0090.250
Hypothesis0.0120.0010.012
LRT0.2640.0140.278
ZlmFit-class1.4040.0641.469
applyFlat0.0020.0000.003
bootVcov10.690.020.71
calcZ1.7180.0471.765
collectResiduals1.5970.0341.632
computeEtFromCt0.0670.0080.075
convertMASTClassicToSingleCellAssay0.1240.0040.128
defaultAssay0.0940.0060.101
defaultPrior0.0010.0000.001
expavg0.0000.0000.001
filterLowExpressedGenes0.1840.0050.189
freq0.0540.0060.060
getConcordance0.3210.0120.333
getwellKey0.0290.0140.042
gseaAfterBoot1.640.021.66
hushWarning0.0010.0000.001
impute2.0060.0352.044
invlogit0.0010.0000.000
logFC0.3550.0090.365
logmean0.0010.0000.001
lrTest1.1490.0391.191
mast_filter1.2720.0151.289
melt.SingleCellAssay0.3040.0090.314
plot.thresholdSCRNACountMatrix1.3050.0361.342
plotSCAConcordance0.8250.0230.849
predict.ZlmFit1.7120.0771.790
se.coef1.6880.0671.756
split-SingleCellAssay-character-method0.5650.0140.579
stat_ell1.6420.0191.663
subset-SingleCellAssay-method0.1440.0040.148
summary-GSEATests-method1.6830.0181.717
summary-ZlmFit-method0.3670.0080.392
thresholdSCRNACountMatrix0.6390.0110.652
waldTest1.6020.0381.642
zlm0.4390.0080.448