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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:00:01 -0400 (Tue, 16 Apr 2019).
| Package 885/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MAST 1.8.2 Andrew McDavid
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: MAST |
| Version: 1.8.2 |
| 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_1.8.2.tar.gz |
| StartedAt: 2019-04-16 01:01:11 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:05:47 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 276.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAST.Rcheck |
| Warnings: 0 |
##############################################################################
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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_1.8.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MAST.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.8.2’
* 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 5.0Mb
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 7.789 5.463 2.336
* 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-3.8-bioc/meat/MAST.Rcheck/00check.log’
for details.
MAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MAST ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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)
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-apple-darwin15.6.0 (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, 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
64.989 39.908 57.532
MAST.Rcheck/MAST-Ex.timings
| name | user | system | elapsed | |
| Drop | 0 | 0 | 0 | |
| FromFlatDF | 2.087 | 1.502 | 1.207 | |
| FromMatrix | 0.200 | 0.015 | 0.217 | |
| Hypothesis | 0.009 | 0.001 | 0.011 | |
| LRT | 0.811 | 0.863 | 0.322 | |
| ZlmFit-class | 3.214 | 0.517 | 1.192 | |
| applyFlat | 0.003 | 0.000 | 0.003 | |
| bootVcov1 | 0.977 | 0.795 | 0.545 | |
| cData | 0.032 | 0.002 | 0.034 | |
| calcZ | 1.854 | 0.918 | 1.327 | |
| collectResiduals | 7.789 | 5.463 | 2.336 | |
| computeEtFromCt | 0.051 | 0.009 | 0.064 | |
| convertMASTClassicToSingleCellAssay | 0.016 | 0.002 | 0.017 | |
| defaultAssay | 0.051 | 0.003 | 0.055 | |
| defaultPrior | 0.002 | 0.000 | 0.002 | |
| expavg | 0.002 | 0.000 | 0.001 | |
| filterLowExpressedGenes | 0.050 | 0.005 | 0.060 | |
| freq | 0.035 | 0.004 | 0.039 | |
| getConcordance | 0.447 | 0.490 | 0.168 | |
| getwellKey | 0.120 | 0.163 | 0.041 | |
| gseaAfterBoot | 1.975 | 1.062 | 1.301 | |
| hushWarning | 0.008 | 0.010 | 0.003 | |
| impute | 2.414 | 1.096 | 1.834 | |
| invlogit | 0.006 | 0.006 | 0.002 | |
| logFC | 0.884 | 0.881 | 0.297 | |
| logmean | 0.008 | 0.010 | 0.003 | |
| lrTest | 1.946 | 0.970 | 1.344 | |
| mast_filter | 0.792 | 0.021 | 0.821 | |
| melt.SingleCellAssay | 0.229 | 0.219 | 0.105 | |
| plot.thresholdSCRNACountMatrix | 0.937 | 0.758 | 0.558 | |
| plotSCAConcordance | 1.595 | 1.579 | 0.644 | |
| predict.ZlmFit | 2.207 | 0.822 | 1.753 | |
| se.coef | 1.490 | 0.949 | 0.929 | |
| split-SingleCellAssay-character-method | 0.074 | 0.002 | 0.077 | |
| stat_ell | 2.231 | 0.820 | 1.793 | |
| subset-SingleCellAssay-method | 0.105 | 0.102 | 0.036 | |
| summary-GSEATests-method | 2.748 | 0.723 | 1.171 | |
| summary-ZlmFit-method | 1.002 | 1.199 | 0.317 | |
| thresholdSCRNACountMatrix | 0.956 | 0.686 | 0.543 | |
| waldTest | 1.217 | 0.803 | 0.801 | |
| zlm | 0.872 | 0.959 | 0.339 | |