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CHECK report for MAST on tokay1

This page was generated on 2019-04-13 11:27:12 -0400 (Sat, 13 Apr 2019).

Package 885/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAST 1.8.2
Andrew McDavid
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 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
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MAST_1.8.2.tar.gz
StartedAt: 2019-04-13 03:32:24 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:38:52 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 388.5 seconds
RetCode: 0
Status:  OK  
CheckDir: MAST.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MAST_1.8.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MAST.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'MAST' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/MAST.Rcheck/00check.log'
for details.



Installation output

MAST.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MAST_1.8.2.tar.gz && rm -rf MAST.buildbin-libdir && mkdir MAST.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MAST.buildbin-libdir MAST_1.8.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MAST_1.8.2.zip && rm MAST_1.8.2.tar.gz MAST_1.8.2.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2325k  100 2325k    0     0  30.1M      0 --:--:-- --:--:-- --:--:-- 31.9M

install for i386

* installing *source* package 'MAST' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MAST'
    finding HTML links ... done
    BayesGLMlike-class                      html  
    Drop                                    html  
    FromFlatDF                              html  
    FromMatrix                              html  
    GLMlike-class                           html  
    GSEATests-class                         html  
    Hypothesis                              html  
    LMERlike-class                          html  
    LMlike-class                            html  
    LRT                                     html  
    MAST-package                            html  
    SceToSingleCellAssay                    html  
    ZlmFit-class                            html  
    applyFlat                               html  
    bootVcov1                               html  
    cData                                   html  
    finding level-2 HTML links ... done

    calcZ                                   html  
    colData-set-SingleCellAssay-DataFrame-method
                                            html  
    collectResiduals                        html  
    computeEtFromCt                         html  
    convertMASTClassicToSingleCellAssay     html  
    defaultAssay                            html  
    defaultPrior                            html  
    dof                                     html  
    ebayes                                  html  
    expavg                                  html  
    fData-methods                           html  
    featureData-methods                     html  
    filterLowExpressedGenes                 html  
    fit                                     html  
    freq                                    html  
    getConcordance                          html  
    getwellKey                              html  
    gseaAfterBoot                           html  
    hushWarning                             html  
    impute                                  html  
    influence.bayesglm                      html  
    invlogit                                html  
    logFC                                   html  
    logmean                                 html  
    lrTest-ZlmFit-character-method          html  
    lrTest                                  html  
    maits-dataset                           html  
    mast_filter                             html  
    melt.SingleCellAssay                    html  
    model.matrix-set                        html  
    model.matrix                            html  
    myBiplot                                html  
    pbootVcov1                              html  
    plot.thresholdSCRNACountMatrix          html  
    plotSCAConcordance                      html  
    plotlrt                                 html  
    predict.ZlmFit                          html  
    primerAverage                           html  
    print.summaryZlmFit                     html  
    read.fluidigm                           html  
    removeResponse                          html  
    rstandard.bayesglm                      html  
    se.coef                                 html  
    show                                    html  
    split-SingleCellAssay-character-method
                                            html  
    stat_ell                                html  
    subset-SingleCellAssay-method           html  
    summarize                               html  
    summary-GSEATests-method                html  
    summary-ZlmFit-method                   html  
    summary.thresholdSCRNACountMatrix       html  
    thresholdSCRNACountMatrix               html  
    vbeta-dataset                           html  
    vbetaFA-dataset                         html  
    waldTest-ZlmFit-matrix-method           html  
    waldTest                                html  
    xform                                   html  
    zlm                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MAST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MAST' as MAST_1.8.2.zip
* DONE (MAST)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MAST' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

MAST.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

Attaching package: 'IRanges'

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

    windows

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 
  30.98    1.53   42.79 

MAST.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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 
  35.76    0.98   48.81 

Example timings

MAST.Rcheck/examples_i386/MAST-Ex.timings

nameusersystemelapsed
Drop000
FromFlatDF0.590.170.66
FromMatrix0.120.000.13
Hypothesis000
LRT0.230.010.25
ZlmFit-class1.460.051.48
applyFlat000
bootVcov10.330.000.33
cData0.030.000.03
calcZ1.110.021.13
collectResiduals2.060.172.17
computeEtFromCt0.060.010.08
convertMASTClassicToSingleCellAssay0.030.000.03
defaultAssay0.060.000.07
defaultPrior0.020.000.01
expavg000
filterLowExpressedGenes0.040.000.05
freq0.050.000.04
getConcordance0.190.000.19
getwellKey0.010.020.03
gseaAfterBoot0.970.000.97
hushWarning000
impute1.420.081.50
invlogit000
logFC0.180.020.19
logmean000
lrTest0.920.060.98
mast_filter0.540.020.56
melt.SingleCellAssay0.050.030.08
plot.thresholdSCRNACountMatrix1.160.031.19
plotSCAConcordance0.550.140.68
predict.ZlmFit1.140.001.14
se.coef0.720.000.71
split-SingleCellAssay-character-method0.090.010.11
stat_ell1.180.041.21
subset-SingleCellAssay-method0.010.010.03
summary-GSEATests-method1.290.031.30
summary-ZlmFit-method0.220.030.25
thresholdSCRNACountMatrix0.880.020.89
waldTest0.510.020.53
zlm0.220.000.22

MAST.Rcheck/examples_x64/MAST-Ex.timings

nameusersystemelapsed
Drop000
FromFlatDF1.160.051.06
FromMatrix0.130.010.14
Hypothesis0.010.000.02
LRT0.280.030.28
ZlmFit-class0.890.000.89
applyFlat000
bootVcov10.410.000.41
cData0.050.000.04
calcZ0.980.000.99
collectResiduals2.640.132.61
computeEtFromCt0.050.000.04
convertMASTClassicToSingleCellAssay0.010.000.02
defaultAssay0.050.000.05
defaultPrior000
expavg000
filterLowExpressedGenes0.050.000.04
freq0.030.000.03
getConcordance0.110.030.13
getwellKey0.010.000.01
gseaAfterBoot1.440.061.50
hushWarning000
impute1.900.001.91
invlogit000
logFC0.280.020.30
logmean000
lrTest0.860.010.87
mast_filter0.910.000.91
melt.SingleCellAssay0.090.020.08
plot.thresholdSCRNACountMatrix0.440.000.44
plotSCAConcordance0.640.000.64
predict.ZlmFit1.750.001.75
se.coef0.920.000.92
split-SingleCellAssay-character-method0.090.000.09
stat_ell1.820.011.83
subset-SingleCellAssay-method0.040.000.05
summary-GSEATests-method1.050.001.04
summary-ZlmFit-method0.200.020.19
thresholdSCRNACountMatrix0.390.000.39
waldTest0.600.050.64
zlm0.200.010.22