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This page was generated on 2018-04-12 13:23:24 -0400 (Thu, 12 Apr 2018).
Package 35/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
AllelicImbalance 1.16.0 Jesper R Gadin
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: AllelicImbalance |
Version: 1.16.0 |
Command: rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.16.0.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.16.0.tar.gz |
StartedAt: 2018-04-11 22:09:21 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 22:19:17 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 596.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: AllelicImbalance.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.16.0.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AllelicImbalance.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'AllelicImbalance/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'AllelicImbalance' version '1.16.0' * 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 ... OK * checking for portable file names ... OK * checking whether package 'AllelicImbalance' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/ASEset-class.Rd:186: missing file link 'RangedSummarizedExperiment' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/ASEset-class.Rd:333: missing file link 'RangedSummarizedExperiment' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/cigar-utilities.Rd:53: missing file link 'GAlignmentsList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/getAlleleCounts.Rd:79: missing file link 'GAlignmentsList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/initialize-ASEset.Rd:125: missing file link 'RangedSummarizedExperiment' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AllelicImbalance.Rcheck/00install.out' for details. * checking installed package size ... OK * 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 ** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed import-bam 12.81 0.02 12.83 annotation-wrappers 8.07 0.17 8.36 lva 5.50 0.00 5.53 ASEset-glocationplot 5.10 0.11 5.21 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed getSnpIdFromLocation 19.22 0.88 25.22 import-bam 16.27 0.29 16.56 annotation-wrappers 8.89 0.28 9.18 lva 5.33 0.03 5.98 ASEset-glocationplot 5.01 0.02 5.03 makeMaskedFasta 0.61 0.02 5.88 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'test-all.R' OK ** running tests for arch 'x64' ... Running 'test-all.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: 1 WARNING See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AllelicImbalance.Rcheck/00check.log' for details.
AllelicImbalance.Rcheck/00install.out
install for i386 * installing *source* package 'AllelicImbalance' ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading Creating a generic function for 'chisq.test' from package 'stats' in package 'AllelicImbalance' Creating a generic function for 'binom.test' from package 'stats' in package 'AllelicImbalance' ** help *** installing help indices converting help for package 'AllelicImbalance' finding HTML links ... done ASEset-barplot html ASEset-class html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/ASEset-class.Rd:186: missing file link 'RangedSummarizedExperiment' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/ASEset-class.Rd:333: missing file link 'RangedSummarizedExperiment' ASEset-filters html ASEset-gbarplot html ASEset-glocationplot html ASEset-gviztrack html ASEset-scanForHeterozygotes html ASEset.old html ASEset.sim html ASEsetFromBam html AllelicImbalance-package html DetectedAI-class html DetectedAI-plot html DetectedAI-summary html GRvariants html GlobalAnalysis-class html LinkVariantAlmlof-class html LinkVariantAlmlof-plot html RegionSummary-class html RiskVariant-class html annotation-wrappers html annotationBarplot html barplot-lattice-support html binom.test html chisq.test html cigar-utilities html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/cigar-utilities.Rd:53: missing file link 'GAlignmentsList' countAllelesFromBam html coverageMatrixListFromGAL html decorateWithExons html decorateWithGenes html defaultMapBias html defaultPhase html detectAI html fractionPlotDf html gba html genomatrix html genotype2phase html getAlleleCounts html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/getAlleleCounts.Rd:79: missing file link 'GAlignmentsList' getAlleleQuality html getAreaFromGeneNames html getDefaultMapBiasExpMean html getSnpIdFromLocation html histplot html implodeList-old html import-bam-2 html import-bam html import-bcf html inferAlleles html inferAltAllele html inferGenotypes html initialize-ASEset html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/initialize-ASEset.Rd:125: missing file link 'RangedSummarizedExperiment' initialize-DetectedAI html initialize-GlobalAnalysis html initialize-RiskVariant html legendBarplot html locationplot html lva html lva.internal html makeMaskedFasta html mapBiasRef html minCountFilt html minFreqFilt html multiAllelicFilt html phase2genotype html phaseArray2phaseMatrix html phaseMatrix2Array html randomRef html reads html refAllele html regionSummary html scanForHeterozygotes-old html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'AllelicImbalance' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'AllelicImbalance' as AllelicImbalance_1.16.0.zip * DONE (AllelicImbalance) In R CMD INSTALL In R CMD INSTALL
AllelicImbalance.Rcheck/tests_i386/test-all.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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("AllelicImbalance") Loading required package: AllelicImbalance Loading required package: grid 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, cbind, colMeans, colSums, colnames, 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: SummarizedExperiment 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 Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following object is masked from 'package:base': apply Loading required package: GenomicAlignments Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:DelayedArray': type The following object is masked from 'package:base': strsplit Loading required package: Rsamtools == testthat results =========================================================== OK: 96 SKIPPED: 1 FAILED: 0 > > > > proc.time() user system elapsed 12.07 0.50 12.71 |
AllelicImbalance.Rcheck/tests_x64/test-all.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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("AllelicImbalance") Loading required package: AllelicImbalance Loading required package: grid 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, cbind, colMeans, colSums, colnames, 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: SummarizedExperiment 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 Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following object is masked from 'package:base': apply Loading required package: GenomicAlignments Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:DelayedArray': type The following object is masked from 'package:base': strsplit Loading required package: Rsamtools == testthat results =========================================================== OK: 96 SKIPPED: 1 FAILED: 0 > > > > proc.time() user system elapsed 15.39 0.42 15.92 |
AllelicImbalance.Rcheck/examples_i386/AllelicImbalance-Ex.timings
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AllelicImbalance.Rcheck/examples_x64/AllelicImbalance-Ex.timings
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