Andrew McDavid
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/MAST |
| Branch: RELEASE_3_10 |
| Last Commit: cd3b54a |
| Last Changed Date: 2019-10-29 13:10:09 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:11:57 -0400 (Wed, 15 Apr 2020).
| Package 961/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MAST 1.12.0 Andrew McDavid
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MAST |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MAST.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MAST_1.12.0.tar.gz |
| StartedAt: 2020-04-15 04:15:02 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:20:42 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 339.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAST.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MAST.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MAST_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/MAST.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
collectResiduals 21.536 0.180 6.803
LRT 7.496 0.032 1.924
summary-ZlmFit-method 6.536 0.028 1.613
FromFlatDF 6.452 0.052 2.703
calcZ 5.540 0.016 2.869
* 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
‘/home/biocbuild/bbs-3.10-bioc/meat/MAST.Rcheck/00check.log’
for details.
MAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MAST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)
MAST.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
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
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 in (function (x, y, weights = rep(1, nobs), start = NULL, etastart = NULL, :
NAs in V(mu)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 279 | SKIPPED: 5 | WARNINGS: 10 | FAILED: 0 ]
>
> proc.time()
user system elapsed
129.384 1.264 85.513
MAST.Rcheck/MAST-Ex.timings
| name | user | system | elapsed | |
| Drop | 0.000 | 0.000 | 0.001 | |
| FromFlatDF | 6.452 | 0.052 | 2.703 | |
| FromMatrix | 0.136 | 0.020 | 0.155 | |
| Hypothesis | 0.008 | 0.000 | 0.008 | |
| LRT | 7.496 | 0.032 | 1.924 | |
| ZlmFit-class | 1.820 | 0.016 | 1.426 | |
| applyFlat | 0.004 | 0.000 | 0.002 | |
| bootVcov1 | 1.072 | 0.004 | 0.770 | |
| cData | 0.168 | 0.072 | 0.241 | |
| calcZ | 5.540 | 0.016 | 2.869 | |
| collectResiduals | 21.536 | 0.180 | 6.803 | |
| computeEtFromCt | 0.044 | 0.004 | 0.051 | |
| convertMASTClassicToSingleCellAssay | 0.048 | 0.000 | 0.051 | |
| defaultAssay | 0.056 | 0.000 | 0.059 | |
| defaultPrior | 0 | 0 | 0 | |
| expavg | 0 | 0 | 0 | |
| filterLowExpressedGenes | 0.096 | 0.000 | 0.097 | |
| freq | 0.044 | 0.000 | 0.043 | |
| getConcordance | 0.672 | 0.008 | 0.339 | |
| getwellKey | 0.012 | 0.004 | 0.014 | |
| gseaAfterBoot | 4.628 | 0.012 | 2.314 | |
| hushWarning | 0.000 | 0.000 | 0.001 | |
| impute | 3.576 | 0.012 | 2.480 | |
| invlogit | 0.004 | 0.000 | 0.000 | |
| logFC | 2.436 | 0.016 | 0.718 | |
| logmean | 0.000 | 0.000 | 0.001 | |
| lrTest | 1.092 | 0.012 | 0.823 | |
| mast_filter | 1.092 | 0.004 | 1.095 | |
| melt.SingleCellAssay | 1.676 | 0.008 | 0.615 | |
| plot.thresholdSCRNACountMatrix | 0.552 | 0.008 | 0.562 | |
| plotSCAConcordance | 1.560 | 0.004 | 0.908 | |
| predict.ZlmFit | 3.076 | 0.008 | 2.116 | |
| se.coef | 1.024 | 0.016 | 0.734 | |
| split-SingleCellAssay-character-method | 0.264 | 0.004 | 0.269 | |
| stat_ell | 3.296 | 0.008 | 2.207 | |
| subset-SingleCellAssay-method | 0.104 | 0.000 | 0.096 | |
| summary-GSEATests-method | 4.644 | 0.028 | 1.926 | |
| summary-ZlmFit-method | 6.536 | 0.028 | 1.613 | |
| thresholdSCRNACountMatrix | 1.252 | 0.016 | 1.271 | |
| waldTest | 1.336 | 0.016 | 1.071 | |
| zlm | 0.932 | 0.000 | 0.505 | |