Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:56 -0400 (Fri, 18 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the MAST package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAST.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1059/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MAST 1.21.3 (landing page) Andrew McDavid
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: MAST |
Version: 1.21.3 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAST.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MAST_1.21.3.tar.gz |
StartedAt: 2022-03-17 19:29:15 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 19:33:15 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 239.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MAST.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAST.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MAST_1.21.3.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MAST.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * 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 '1.21.3' * 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 whether package 'MAST' can be installed ... OK * checking installed package size ... NOTE installed size is 5.5Mb 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 LazyData ... 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: 2 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/MAST.Rcheck/00check.log' for details.
MAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MAST ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-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 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-defunct html finding level-2 HTML links ... done MAST-package html SceToSingleCellAssay html ZlmFit-class html applyFlat html bootVcov1 html calcZ html colData-set-SingleCellAssay-DataFrame-method html collectResiduals html computeEtFromCt html convertMASTClassicToSingleCellAssay html defaultAssay html defaultPrior html dof html ebayes html expavg 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 meld_list_left html melt.SingleCellAssay html model.matrix-set html model.matrix html myBiplot 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 * DONE (MAST) Making 'packages.html' ... done
MAST.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" Copyright (C) 2021 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: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname 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")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians 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 : grouping factors must have > 1 sampled level NULL NULL NULL Error in (function (x, y, weights = rep.int(1, nobs), start = NULL, etastart = NULL, : NAs in V(mu) [ FAIL 0 | WARN 3 | SKIP 5 | PASS 293 ] == Skipped tests =============================================================== * empty test (5) [ FAIL 0 | WARN 3 | SKIP 5 | PASS 293 ] > > proc.time() user system elapsed 46.68 1.56 58.67
MAST.Rcheck/MAST-Ex.timings
name | user | system | elapsed | |
Drop | 0 | 0 | 0 | |
FromFlatDF | 0.91 | 0.06 | 0.96 | |
FromMatrix | 0.20 | 0.05 | 0.25 | |
Hypothesis | 0 | 0 | 0 | |
LRT | 0.10 | 0.03 | 0.14 | |
ZlmFit-class | 1.08 | 0.00 | 1.08 | |
applyFlat | 0 | 0 | 0 | |
bootVcov1 | 0.44 | 0.02 | 0.45 | |
calcZ | 0.79 | 0.03 | 0.82 | |
collectResiduals | 0.75 | 0.00 | 0.75 | |
computeEtFromCt | 0.05 | 0.00 | 0.05 | |
convertMASTClassicToSingleCellAssay | 0.23 | 0.00 | 0.23 | |
defaultAssay | 0.02 | 0.01 | 0.04 | |
defaultPrior | 0 | 0 | 0 | |
expavg | 0 | 0 | 0 | |
filterLowExpressedGenes | 0.2 | 0.0 | 0.2 | |
freq | 0.02 | 0.00 | 0.01 | |
getConcordance | 0.34 | 0.00 | 0.35 | |
getwellKey | 0.02 | 0.00 | 0.01 | |
gseaAfterBoot | 0.84 | 0.02 | 0.86 | |
hushWarning | 0 | 0 | 0 | |
impute | 0.92 | 0.00 | 0.93 | |
invlogit | 0 | 0 | 0 | |
logFC | 0.24 | 0.00 | 0.23 | |
logmean | 0 | 0 | 0 | |
lrTest | 0.57 | 0.00 | 0.56 | |
mast_filter | 1.26 | 0.03 | 1.29 | |
meld_list_left | 0 | 0 | 0 | |
melt.SingleCellAssay | 0.31 | 0.00 | 0.32 | |
plot.thresholdSCRNACountMatrix | 0.38 | 0.05 | 0.43 | |
plotSCAConcordance | 0.83 | 0.03 | 0.86 | |
predict.ZlmFit | 0.84 | 0.00 | 0.85 | |
se.coef | 0.84 | 0.00 | 0.86 | |
split-SingleCellAssay-character-method | 1.10 | 0.04 | 1.14 | |
stat_ell | 0.80 | 0.00 | 0.79 | |
subset-SingleCellAssay-method | 0.17 | 0.00 | 0.18 | |
summary-GSEATests-method | 0.89 | 0.02 | 0.91 | |
summary-ZlmFit-method | 0.39 | 0.02 | 0.40 | |
thresholdSCRNACountMatrix | 0.86 | 0.01 | 0.88 | |
waldTest | 0.52 | 0.02 | 0.62 | |
zlm | 0.28 | 0.00 | 0.29 | |