Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:36:59 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MAST_1.10.0.tar.gz |
StartedAt: 2019-10-16 04:56:57 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 05:03:54 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 416.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MAST.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MAST_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MAST.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '1.10.0' * 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 whether package 'MAST' can be installed ... OK * checking installed package size ... NOTE installed size is 5.4Mb 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MAST.Rcheck/00check.log' for details.
MAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MAST_1.10.0.tar.gz && rm -rf MAST.buildbin-libdir && mkdir MAST.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MAST.buildbin-libdir MAST_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MAST_1.10.0.zip && rm MAST_1.10.0.tar.gz MAST_1.10.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 5935k 100 5935k 0 0 26.2M 0 --:--:-- --:--:-- --:--:-- 27.0M install for i386 * 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-package html SceToSingleCellAssay html ZlmFit-class html applyFlat html bootVcov1 html cData html finding level-2 HTML links ... done calcZ html colData-set-SingleCellAssay-DataFrame-method html collectResiduals html computeEtFromCt html convertMASTClassicToSingleCellAssay html defaultAssay html defaultPrior html dof html ebayes html expavg html fData-methods html featureData-methods 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 melt.SingleCellAssay html model.matrix-set html model.matrix html myBiplot html pbootVcov1 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 install for x64 * installing *source* package 'MAST' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'MAST' as MAST_1.10.0.zip * DONE (MAST) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'MAST' successfully unpacked and MD5 sums checked
MAST.Rcheck/tests_i386/testthat.Rout R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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 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")'. 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 41.26 1.76 58.54 |
MAST.Rcheck/tests_x64/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-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: 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 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")'. 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 39.12 1.31 56.85 |
MAST.Rcheck/examples_i386/MAST-Ex.timings
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MAST.Rcheck/examples_x64/MAST-Ex.timings
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