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CHECK report for MAST on tokay2

This page was generated on 2019-10-16 12:36:59 -0400 (Wed, 16 Oct 2019).

Package 924/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAST 1.10.0
Andrew McDavid
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MAST
Branch: RELEASE_3_9
Last Commit: 7223e4f
Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MAST
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MAST_1.10.0.tar.gz
StartedAt: 2019-10-16 04:56:57 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:03:54 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 416.8 seconds
RetCode: 0
Status:  OK  
CheckDir: MAST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MAST_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MAST.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.10.0'
* 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 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-3.9-bioc/meat/MAST.Rcheck/00check.log'
for details.



Installation output

MAST.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MAST_1.10.0.tar.gz && rm -rf MAST.buildbin-libdir && mkdir MAST.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MAST.buildbin-libdir MAST_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MAST_1.10.0.zip && rm MAST_1.10.0.tar.gz MAST_1.10.0.zip
###
##############################################################################
##############################################################################


  % 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 5935k  100 5935k    0     0  26.2M      0 --:--:-- --:--:-- --:--:-- 27.0M

install for i386

* 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
  converting help for package 'MAST'
    finding HTML links ... done
    BayesGLMlike-class                      html  
    CovFromBoots                            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  
    predicted_sig-dataset                   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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MAST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MAST' as MAST_1.10.0.zip
* DONE (MAST)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MAST' successfully unpacked and MD5 sums checked

Tests output

MAST.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, 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

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, rowsum


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 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  41.26    1.76   58.54 

MAST.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, 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

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, rowsum


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 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  39.12    1.31   56.85 

Example timings

MAST.Rcheck/examples_i386/MAST-Ex.timings

nameusersystemelapsed
Drop000
FromFlatDF0.700.020.75
FromMatrix0.170.000.17
Hypothesis0.000.010.02
LRT0.250.050.26
ZlmFit-class0.970.000.97
applyFlat000
bootVcov10.410.030.44
cData0.010.020.03
calcZ0.940.000.96
collectResiduals2.410.142.47
computeEtFromCt0.070.000.07
convertMASTClassicToSingleCellAssay0.020.000.02
defaultAssay0.050.000.05
defaultPrior000
expavg000
filterLowExpressedGenes0.010.030.04
freq0.020.020.03
getConcordance0.110.030.14
getwellKey0.030.000.04
gseaAfterBoot1.810.071.86
hushWarning000
impute1.170.021.18
invlogit000
logFC0.220.030.25
logmean000
lrTest0.810.080.89
mast_filter0.570.020.58
melt.SingleCellAssay0.070.000.08
plot.thresholdSCRNACountMatrix0.430.030.45
plotSCAConcordance0.530.000.51
predict.ZlmFit1.640.001.64
se.coef0.790.030.82
split-SingleCellAssay-character-method0.070.010.09
stat_ell1.160.001.16
subset-SingleCellAssay-method0.030.020.04
summary-GSEATests-method1.330.011.35
summary-ZlmFit-method0.310.040.29
thresholdSCRNACountMatrix2.020.032.05
waldTest1.510.111.63
zlm0.220.010.23

MAST.Rcheck/examples_x64/MAST-Ex.timings

nameusersystemelapsed
Drop000
FromFlatDF0.800.080.87
FromMatrix0.20.00.2
Hypothesis0.020.000.02
LRT0.330.010.31
ZlmFit-class1.760.071.83
applyFlat000
bootVcov10.540.010.55
cData0.030.020.04
calcZ1.360.031.41
collectResiduals2.370.202.53
computeEtFromCt0.080.000.08
convertMASTClassicToSingleCellAssay0.030.000.03
defaultAssay0.060.000.06
defaultPrior000
expavg000
filterLowExpressedGenes0.050.020.07
freq0.030.010.04
getConcordance0.170.000.17
getwellKey0.030.000.04
gseaAfterBoot1.320.071.29
hushWarning000
impute2.060.032.10
invlogit000
logFC0.260.010.28
logmean000
lrTest0.880.050.92
mast_filter0.750.000.75
melt.SingleCellAssay0.080.000.08
plot.thresholdSCRNACountMatrix1.140.001.14
plotSCAConcordance0.540.000.53
predict.ZlmFit1.700.001.71
se.coef0.640.000.64
split-SingleCellAssay-character-method0.060.000.06
stat_ell1.750.001.75
subset-SingleCellAssay-method0.010.000.01
summary-GSEATests-method0.880.000.88
summary-ZlmFit-method0.220.000.22
thresholdSCRNACountMatrix1.110.061.17
waldTest1.430.031.47
zlm0.270.020.28