Andrew McDavid
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/MAST |
| Branch: RELEASE_3_7 |
| Last Commit: 40d5fc6 |
| Last Changed Date: 2018-05-09 14:44:28 -0400 (Wed, 09 May 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:57:16 -0400 (Wed, 17 Oct 2018).
| Package 836/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MAST 1.6.1 Andrew McDavid
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: MAST |
| Version: 1.6.1 |
| 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_1.6.1.tar.gz |
| StartedAt: 2018-10-16 22:23:09 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 22:27:35 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 265.7 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_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MAST.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.6.1’
* 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 ... NOTE
assay_idx: no visible global function definition for ‘assayNames’
collectResiduals: no visible global function definition for
‘assayNames’
collectResiduals: no visible global function definition for ‘assay<-’
collectResiduals: no visible global function definition for
‘assayNames<-’
primerAverage: no visible global function definition for ‘assay<-’
primerAverage: no visible global function definition for ‘rowData<-’
assay<-,SingleCellAssay-missing: no visible global function definition
for ‘assay<-’
assayNames<-,SingleCellAssay-character: no visible global function
definition for ‘assayNames’
assayNames<-,SingleCellAssay-character: no visible global function
definition for ‘assays<-’
exprs<-,SingleCellAssay-ANY: no visible global function definition for
‘assay<-’
Undefined global functions or variables:
assay<- assayNames assayNames<- assays<- rowData<-
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.7-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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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: 278 SKIPPED: 5 FAILED: 0
>
> proc.time()
user system elapsed
49.973 10.846 56.897
MAST.Rcheck/MAST-Ex.timings
| name | user | system | elapsed | |
| Drop | 0.002 | 0.000 | 0.002 | |
| FromFlatDF | 1.826 | 1.454 | 1.147 | |
| FromMatrix | 0.227 | 0.022 | 0.256 | |
| Hypothesis | 0.020 | 0.002 | 0.023 | |
| LRT | 0.211 | 0.017 | 0.231 | |
| ZlmFit-class | 0.862 | 0.062 | 0.932 | |
| applyFlat | 0.005 | 0.001 | 0.004 | |
| bootVcov1 | 0.471 | 0.021 | 0.503 | |
| cData | 0.027 | 0.001 | 0.030 | |
| calcZ | 1.145 | 0.031 | 1.184 | |
| collectResiduals | 4.485 | 0.289 | 1.975 | |
| computeEtFromCt | 0.066 | 0.010 | 0.078 | |
| convertMASTClassicToSingleCellAssay | 0.015 | 0.002 | 0.018 | |
| defaultAssay | 0.034 | 0.003 | 0.037 | |
| defaultPrior | 0.001 | 0.000 | 0.002 | |
| expavg | 0.001 | 0.000 | 0.002 | |
| filterLowExpressedGenes | 0.044 | 0.003 | 0.048 | |
| freq | 0.033 | 0.006 | 0.038 | |
| getConcordance | 0.149 | 0.014 | 0.164 | |
| getwellKey | 0.022 | 0.006 | 0.027 | |
| gseaAfterBoot | 1.037 | 0.030 | 1.054 | |
| hushWarning | 0.010 | 0.009 | 0.003 | |
| impute | 2.322 | 0.682 | 1.930 | |
| invlogit | 0.011 | 0.001 | 0.002 | |
| logFC | 1.109 | 0.075 | 0.254 | |
| logmean | 0.009 | 0.001 | 0.002 | |
| lrTest | 1.209 | 0.081 | 0.788 | |
| mast_filter | 1.241 | 0.024 | 1.277 | |
| melt.SingleCellAssay | 0.092 | 0.005 | 0.097 | |
| plot.thresholdSCRNACountMatrix | 0.549 | 0.043 | 0.599 | |
| plotSCAConcordance | 0.558 | 0.022 | 0.583 | |
| predict.ZlmFit | 1.722 | 0.016 | 1.751 | |
| se.coef | 1.650 | 0.065 | 0.771 | |
| split-SingleCellAssay-character-method | 0.100 | 0.004 | 0.108 | |
| stat_ell | 1.928 | 0.010 | 1.955 | |
| subset-SingleCellAssay-method | 0.256 | 0.035 | 0.052 | |
| summary-GSEATests-method | 1.735 | 0.096 | 1.162 | |
| summary-ZlmFit-method | 1.37 | 0.52 | 0.28 | |
| thresholdSCRNACountMatrix | 1.679 | 0.238 | 1.077 | |
| waldTest | 0.738 | 0.018 | 0.759 | |
| zlm | 0.231 | 0.006 | 0.241 | |