Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:09:47 -0400 (Wed, 16 Oct 2019).
Package 924/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
MAST 1.10.0 Andrew McDavid
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: MAST |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MAST.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MAST_1.10.0.tar.gz |
StartedAt: 2019-10-16 02:54:09 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 02:59:07 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 298.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MAST.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MAST.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MAST_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MAST.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘1.10.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘MAST’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.1Mb 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 18.887 0.089 4.886 LRT 6.974 0.035 1.120 summary-ZlmFit-method 6.019 0.024 1.314 FromFlatDF 5.426 0.102 1.800 * 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-3.9-bioc/meat/MAST.Rcheck/00check.log’ for details.
MAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MAST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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 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 106.678 1.197 68.292
MAST.Rcheck/MAST-Ex.timings
name | user | system | elapsed | |
Drop | 0.000 | 0.000 | 0.001 | |
FromFlatDF | 5.426 | 0.102 | 1.800 | |
FromMatrix | 0.117 | 0.000 | 0.117 | |
Hypothesis | 0.007 | 0.000 | 0.007 | |
LRT | 6.974 | 0.035 | 1.120 | |
ZlmFit-class | 1.262 | 0.004 | 0.819 | |
applyFlat | 0.002 | 0.000 | 0.001 | |
bootVcov1 | 0.705 | 0.008 | 0.424 | |
cData | 0.048 | 0.000 | 0.049 | |
calcZ | 4.108 | 0.028 | 1.749 | |
collectResiduals | 18.887 | 0.089 | 4.886 | |
computeEtFromCt | 0.036 | 0.000 | 0.036 | |
convertMASTClassicToSingleCellAssay | 0.013 | 0.000 | 0.013 | |
defaultAssay | 0.03 | 0.00 | 0.03 | |
defaultPrior | 0.000 | 0.000 | 0.001 | |
expavg | 0.001 | 0.000 | 0.000 | |
filterLowExpressedGenes | 0.028 | 0.000 | 0.028 | |
freq | 0.020 | 0.000 | 0.019 | |
getConcordance | 0.506 | 0.000 | 0.155 | |
getwellKey | 0.014 | 0.000 | 0.014 | |
gseaAfterBoot | 4.797 | 0.016 | 1.765 | |
hushWarning | 0.001 | 0.000 | 0.001 | |
impute | 2.723 | 0.028 | 1.727 | |
invlogit | 0.002 | 0.000 | 0.001 | |
logFC | 2.122 | 0.012 | 0.540 | |
logmean | 0.001 | 0.000 | 0.001 | |
lrTest | 1.053 | 0.020 | 0.816 | |
mast_filter | 0.705 | 0.000 | 0.705 | |
melt.SingleCellAssay | 1.100 | 0.008 | 0.241 | |
plot.thresholdSCRNACountMatrix | 0.565 | 0.040 | 0.605 | |
plotSCAConcordance | 1.361 | 0.004 | 0.726 | |
predict.ZlmFit | 2.454 | 0.008 | 1.435 | |
se.coef | 1.166 | 0.004 | 0.883 | |
split-SingleCellAssay-character-method | 0.095 | 0.000 | 0.094 | |
stat_ell | 2.926 | 0.004 | 1.917 | |
subset-SingleCellAssay-method | 0.024 | 0.000 | 0.019 | |
summary-GSEATests-method | 4.737 | 0.052 | 2.500 | |
summary-ZlmFit-method | 6.019 | 0.024 | 1.314 | |
thresholdSCRNACountMatrix | 0.504 | 0.024 | 0.529 | |
waldTest | 1.035 | 0.008 | 0.817 | |
zlm | 0.773 | 0.004 | 0.358 | |