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This page was generated on 2020-10-17 11:56:41 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE GGtools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 731/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GGtools 5.24.0 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK |
Package: GGtools |
Version: 5.24.0 |
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GGtools.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GGtools_5.24.0.tar.gz |
StartedAt: 2020-10-17 04:30:58 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 04:53:04 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 1326.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GGtools.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GGtools.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GGtools_5.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GGtools.Rcheck' * using R version 4.0.3 (2020-10-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'GGtools/DESCRIPTION' ... OK * this is package 'GGtools' version '5.24.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: 'MatrixEQTL' * 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 'GGtools' can be installed ... OK * checking installed package size ... NOTE installed size is 72.2Mb sub-directories of 1Mb or more: R 1.0Mb data 27.0Mb parts 2.0Mb pup 2.0Mb rdas 10.3Mb vcf 28.8Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... NOTE 'library' or 'require' call to 'Homo.sapiens' which was already attached by Depends. Please remove these calls from your code. Packages in Depends field not imported from: 'Homo.sapiens' 'parallel' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plot,gwSnpScreenResult-character: warning in axis(3, at = genePosition(x@gene, annlib = x@annotation), col = "red", lwd = 2, label = " "): partial argument match of 'label' to 'labels' .summarize: no visible binding for global variable 'npc' .summarize: no visible binding for global variable 'maf' .summarize: no visible binding for global variable 'radiusUsed' .summarize: no visible binding for global variable 'excl' .transTab: no visible global function definition for 'snpsBySeqname' SnpMatrixCisToSummex: no visible global function definition for 'rowRanges' add878: no visible binding for global variable 'hmm878' addcadd: no visible binding for global variable 'bindcadd' addcadd: no visible global function definition for '%dopar%' addcadd: no visible global function definition for 'foreach' addcadd: no visible binding for global variable 'x' addgwhit: no visible binding for global variable 'gwastagger' addgwhit: no visible global function definition for 'overlapsAny' appraise : .redu.fdr: no visible global function definition for 'setkey' appraise : .redu.fdr: no visible binding for global variable 'snp' appraise : .redu.fdr: no visible binding for global variable '.N' appraise : .redu.fdr : <anonymous>: no visible global function definition for 'setkeyv' appraise : .redu.fdr : <anonymous>: no visible binding for global variable '.N' appraise : .discmods: no visible global function definition for '%dopar%' appraise : .discmods: no visible global function definition for 'foreach' buildConfList : z : <anonymous>: no visible binding for global variable 'pl' cgff2dt: no visible global function definition for '%dopar%' cgff2dt: no visible global function definition for 'foreach' cgff2dt: no visible global function definition for 'as.data.table' cgff2dt: no visible binding for global variable 'hmm878' cgff2dt: no visible global function definition for 'overlapsAny' cgff2dt: no visible binding for global variable 'gwastagger' cisAssoc: no visible global function definition for 'rowRanges' cisAssoc: no visible global function definition for 'assays' cisAssoc: no visible global function definition for 'colData' cisAssoc: no visible binding for global variable 'chi.squared' ciseqByCluster : <anonymous>: no visible global function definition for 'detectCores' ciseqByCluster: no visible binding for '<<-' assignment to 'firstHalf' ciseqByCluster: no visible binding for '<<-' assignment to 'secondHalf' ciseqByCluster: no visible binding for '<<-' assignment to 'firstThird' ciseqByCluster: no visible binding for '<<-' assignment to 'lastThird' ciseqByCluster: no visible binding for '<<-' assignment to 'midThird' ciseqByCluster : setupSplit : <anonymous>: no visible binding for global variable 'mclapply' ciseqByCluster: no visible binding for '<<-' assignment to 'runOneSplit' ciseqByCluster : <anonymous>: no visible binding for global variable 'firstHalf' ciseqByCluster : <anonymous> : cr2gff: no visible global function definition for 'ranges<-' ciseqByCluster : <anonymous> : cr2gff: no visible global function definition for 'export.gff3' ciseqByCluster: no visible binding for global variable 'firstThird' ciseqByCluster: no visible binding for global variable 'midThird' ciseqByCluster: no visible binding for global variable 'lastThird' ciseqByCluster : <anonymous>: no visible global function definition for 'runOneSplit' eqBox: no visible global function definition for 'assay' eqDesc: no visible global function definition for 'assay' eqsens_dt: no visible global function definition for 'setnames' eqsens_dt: no visible global function definition for '%dopar%' eqsens_dt: no visible global function definition for 'foreach' eqsens_dt: no visible binding for global variable 'curp' eqtlTests.me: no visible binding for global variable 'modelLINEAR' eqtlTests.me: no visible binding for global variable 'SlicedData' eqtlTests.me: no visible binding for global variable 'Matrix_eQTL_engine' eqtlTests.meText: no visible binding for global variable 'modelLINEAR' eqtlTests.meText: no visible binding for global variable 'SlicedData' eqtlTests.meText: no visible binding for global variable 'Matrix_eQTL_engine' fplot: no visible global function definition for 'forestplot' genemodel: no visible global function definition for 'select' genemodel: no visible binding for global variable 'Homo.sapiens' getAsSlicedData: no visible binding for global variable 'target' getCisMap: no visible global function definition for 'snpsBySeqname' get_probechunks: no visible global function definition for 'select' inflammFilter: no visible binding for global variable 'gwrngs' inflammFilter: no visible global function definition for 'overlapsAny' makeSeqinfo: no visible binding for global variable 'hg19.si.df' plotsens: no visible binding for global variable 'mafs' plotsens: no visible binding for global variable 'value' plotsens: no visible binding for global variable 'FDR' pullHits: no visible global function definition for 'ranges<-' richNull : <anonymous>: no visible global function definition for 'bindmaf' simpleTiling: no visible binding for global variable 'Homo.sapiens' simpleTiling: no visible global function definition for 'tileGenome' topKfeats: no visible binding for global variable 'i1' topKfeats: no visible binding for global variable 'i2' tscan2df: no visible global function definition for '%dopar%' tscan2df: no visible global function definition for 'foreach' tscan2df: no visible binding for global variable 'i' tscan2gr: no visible global function definition for '%dopar%' tscan2gr: no visible global function definition for 'foreach' tscan2gr: no visible binding for global variable 'i' waldtests : <anonymous>: no visible global function definition for 'wald.test' plot,gwSnpScreenResult-character: no visible global function definition for 'snpcount' plot,gwSnpScreenResult-character: no visible global function definition for 'snpsBySeqname' Undefined global functions or variables: %dopar% .N FDR Homo.sapiens Matrix_eQTL_engine SlicedData as.data.table assay assays bindcadd bindmaf chi.squared colData curp detectCores excl export.gff3 firstHalf firstThird foreach forestplot gwastagger gwrngs hg19.si.df hmm878 i i1 i2 lastThird maf mafs mclapply midThird modelLINEAR npc overlapsAny pl radiusUsed ranges<- rowRanges runOneSplit select setkey setkeyv setnames snp snpcount snpsBySeqname target tileGenome value wald.test x * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: 'MatrixEQTL' * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed cisAssoc 49.35 2.37 58.74 eqtlTests 11.34 1.21 28.84 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cisAssoc 45.07 1.32 46.39 eqtlTests 9.72 0.87 18.11 gwSnpTests 3.22 0.09 8.13 pifdr 1.81 0.06 11.60 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'cis.R' Running 'eqvgwst.R' Running 'test.meqtlTests.R' Running 'test.meta.trans.R' Running 'testCisMap.R' Running 'testTrans.R' ERROR Running the tests in 'tests/testTrans.R' failed. Last 13 lines of output: > schrpref(tconf) = "ch" > exFilter(tconf) = function(x)x > gchrpref = "" > batchsize(tconf) = 200L > > suppressPackageStartupMessages(library(GGtools)) > > t1 = transScores(tconf) Loading required package: illuminaHumanv1.db opening ff C:/Users/biocbuild/bbs-3.11-bioc/meat/GGtools.Rcheck/tests_i386/cisScratch22/tsc_20_chr22.ff 2opening ff C:/Users/biocbuild/bbs-3.11-bioc/meat/GGtools.Rcheck/tests_i386/cisScratch22/tsctmp2_chr22.ff Error in get(".rambytes") : object '.rambytes' not found Calls: transScores -> updateKfeats -> chunk -> chunk.default -> get Execution halted ** running tests for arch 'x64' ... Running 'cis.R' Running 'eqvgwst.R' Running 'test.meqtlTests.R' Running 'test.meta.trans.R' Running 'testCisMap.R' Running 'testTrans.R' ERROR Running the tests in 'tests/testTrans.R' failed. Last 13 lines of output: > schrpref(tconf) = "ch" > exFilter(tconf) = function(x)x > gchrpref = "" > batchsize(tconf) = 200L > > suppressPackageStartupMessages(library(GGtools)) > > t1 = transScores(tconf) Loading required package: illuminaHumanv1.db opening ff C:/Users/biocbuild/bbs-3.11-bioc/meat/GGtools.Rcheck/tests_x64/cisScratch22/tsc_20_chr22.ff 2opening ff C:/Users/biocbuild/bbs-3.11-bioc/meat/GGtools.Rcheck/tests_x64/cisScratch22/tsctmp2_chr22.ff Error in get(".rambytes") : object '.rambytes' not found Calls: transScores -> updateKfeats -> chunk -> chunk.default -> get Execution halted * 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 ERRORs, 6 NOTEs See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GGtools.Rcheck/00check.log' for details.
GGtools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/GGtools_5.24.0.tar.gz && rm -rf GGtools.buildbin-libdir && mkdir GGtools.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GGtools.buildbin-libdir GGtools_5.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL GGtools_5.24.0.zip && rm GGtools_5.24.0.tar.gz GGtools_5.24.0.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 7 69.2M 7 5392k 0 0 10.0M 0 0:00:06 --:--:-- 0:00:06 10.1M 100 69.2M 100 69.2M 0 0 56.0M 0 0:00:01 0:00:01 --:--:-- 56.2M install for i386 * installing *source* package 'GGtools' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GGtools' finding HTML links ... done All.cis html CisConfig-class html finding level-2 HTML links ... done EqAppr-class html GGtools-package html TransConfig-class html appraise html b1 html best.cis.eQTLs html best.trans.eQTLs html bindmaf html cgff2dt html cisAssoc html cisRun-class html ciseqByCluster html collectBest html concatCis html eqBox html eqsens_dt html eqtlTests html eqtlTests.me html eqtlTestsManager-class html ex html getCisMap html gffprocess html gwSnpTests html hmm878 html pifdr html qqhex html richNull html sampsInVCF html scoresCis html sensanal html sensiCisInput-class html sensiCisOutput-class html simpleTiling html snplocsDefault html strMultPop html transManager-class html transScores html transTab html transeqByCluster html vcf2sm 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 'GGtools' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'GGtools' as GGtools_5.24.0.zip * DONE (GGtools) * installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library' package 'GGtools' successfully unpacked and MD5 sums checked
GGtools.Rcheck/tests_i386/cis.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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. > > suppressPackageStartupMessages(library(GGtools)) > > # configure > cc = new("CisConfig") > chrnames(cc) = "21" > genome(cc) = "hg19" > nperm(cc) = 2L > lkp = try(library(parallel)) > if (!inherits(lkp, "try-error")) { + nc = min(10, detectCores()) + options(mc.cores=nc) + geneApply(cc) = mclapply + } > estimates(cc) = FALSE > set.seed(1234) > # system.time(f1 <- cisScores( cc )) > # > # demonstrate adding annotation on chromatin state and gwas status > # > eprops = function(ans) { + # + # only adds fields to values() of the input + # + data(hmm878) + ac = as.character + eqr = GRanges(ac(seqnames(ans)), IRanges(ans$snplocs, width=1)) + fo = findOverlaps(eqr, hmm878) + chromcat878 = factor(rep("none", length(ans)), levels=c(unique(hmm878$name), "none")) + chromcat878[ queryHits(fo) ] = factor(hmm878$name[subjectHits(fo)]) + ans$chromcat878 = chromcat878 + + if (require(gwascat)) { + data(gwastagger) + isgwashit = 1*(overlapsAny(eqr, gwastagger) | ans$snp %in% gwastagger$tagid) # allow match by loc or name + ans$isgwashit = isgwashit + } + ans + } > extraProps(cc) = eprops > set.seed(1234) > rhs(cc) = ~1-1 > if (.Platform$OS.type != "windows") { + (f2 <- cisScores( cc )) + isTRUE(sum(f2$fdr < 0.05) == 172) # can change with annotation or location changes, check serialized results if necessary + } > TRUE [1] TRUE > > proc.time() user system elapsed 17.21 1.57 22.03 |
GGtools.Rcheck/tests_x64/cis.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > suppressPackageStartupMessages(library(GGtools)) > > # configure > cc = new("CisConfig") > chrnames(cc) = "21" > genome(cc) = "hg19" > nperm(cc) = 2L > lkp = try(library(parallel)) > if (!inherits(lkp, "try-error")) { + nc = min(10, detectCores()) + options(mc.cores=nc) + geneApply(cc) = mclapply + } > estimates(cc) = FALSE > set.seed(1234) > # system.time(f1 <- cisScores( cc )) > # > # demonstrate adding annotation on chromatin state and gwas status > # > eprops = function(ans) { + # + # only adds fields to values() of the input + # + data(hmm878) + ac = as.character + eqr = GRanges(ac(seqnames(ans)), IRanges(ans$snplocs, width=1)) + fo = findOverlaps(eqr, hmm878) + chromcat878 = factor(rep("none", length(ans)), levels=c(unique(hmm878$name), "none")) + chromcat878[ queryHits(fo) ] = factor(hmm878$name[subjectHits(fo)]) + ans$chromcat878 = chromcat878 + + if (require(gwascat)) { + data(gwastagger) + isgwashit = 1*(overlapsAny(eqr, gwastagger) | ans$snp %in% gwastagger$tagid) # allow match by loc or name + ans$isgwashit = isgwashit + } + ans + } > extraProps(cc) = eprops > set.seed(1234) > rhs(cc) = ~1-1 > if (.Platform$OS.type != "windows") { + (f2 <- cisScores( cc )) + isTRUE(sum(f2$fdr < 0.05) == 172) # can change with annotation or location changes, check serialized results if necessary + } > TRUE [1] TRUE > > proc.time() user system elapsed 18.60 0.79 22.61 |
GGtools.Rcheck/tests_i386/eqvgwst.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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. > > # april 2011/jan 2012 > # compares gwSnpTests to eqtlTests > library(GGtools) Loading required package: GGBase Loading required package: snpStats Loading required package: survival Loading required package: Matrix Loading required package: data.table Loading required package: parallel Loading required package: Homo.sapiens Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics 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 object is masked from 'package:Matrix': which 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: 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: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:data.table': first, second The following object is masked from 'package:Matrix': expand The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:data.table': shift The following object is masked from 'package:grDevices': windows Loading required package: OrganismDbi Loading required package: GenomicFeatures Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: GO.db Loading required package: org.Hs.eg.db Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene Attaching package: 'GGtools' The following object is masked from 'package:stats': getCall > hmceuB36.2021 <- getSS("GGtools", c("20")) > library(illuminaHumanv1.db) > cp = get("CPNE1", revmap(illuminaHumanv1SYMBOL)) > hcp = hmceuB36.2021[ probeId(cp), ] > t1 = gwSnpTests(genesym("CPNE1")~male, hcp) > pick = as(t1@.Data[[1]], "data.frame")[22101:22115,] > rsids = rownames(pick)[!is.na(pick[,1])] > csq = pick[rsids,1] > names(csq) = rsids > fi = tempfile() > if (file.exists(fi)) unlink(fi, recursive=TRUE) > t2 = eqtlTests(hcp, ~male, targdir=fi) > sco = t2[rsids,][,1] > unlink(fi, recursive=TRUE) > comp = (sco-trunc(100*csq,0)/100)/sco > (!(max(abs(comp)) > .01)) [1] TRUE > > > proc.time() user system elapsed 26.48 2.87 32.67 |
GGtools.Rcheck/tests_x64/eqvgwst.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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. > > # april 2011/jan 2012 > # compares gwSnpTests to eqtlTests > library(GGtools) Loading required package: GGBase Loading required package: snpStats Loading required package: survival Loading required package: Matrix Loading required package: data.table Loading required package: parallel Loading required package: Homo.sapiens Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics 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 object is masked from 'package:Matrix': which 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: 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: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:data.table': first, second The following object is masked from 'package:Matrix': expand The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:data.table': shift The following object is masked from 'package:grDevices': windows Loading required package: OrganismDbi Loading required package: GenomicFeatures Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: GO.db Loading required package: org.Hs.eg.db Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene Attaching package: 'GGtools' The following object is masked from 'package:stats': getCall > hmceuB36.2021 <- getSS("GGtools", c("20")) > library(illuminaHumanv1.db) > cp = get("CPNE1", revmap(illuminaHumanv1SYMBOL)) > hcp = hmceuB36.2021[ probeId(cp), ] > t1 = gwSnpTests(genesym("CPNE1")~male, hcp) > pick = as(t1@.Data[[1]], "data.frame")[22101:22115,] > rsids = rownames(pick)[!is.na(pick[,1])] > csq = pick[rsids,1] > names(csq) = rsids > fi = tempfile() > if (file.exists(fi)) unlink(fi, recursive=TRUE) > t2 = eqtlTests(hcp, ~male, targdir=fi) > sco = t2[rsids,][,1] > unlink(fi, recursive=TRUE) > comp = (sco-trunc(100*csq,0)/100)/sco > (!(max(abs(comp)) > .01)) [1] TRUE > > > proc.time() user system elapsed 25.89 1.93 31.50 |
GGtools.Rcheck/tests_i386/test.meqtlTests.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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(GGtools) Loading required package: GGBase Loading required package: snpStats Loading required package: survival Loading required package: Matrix Loading required package: data.table Loading required package: parallel Loading required package: Homo.sapiens Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics 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 object is masked from 'package:Matrix': which 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: 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: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:data.table': first, second The following object is masked from 'package:Matrix': expand The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:data.table': shift The following object is masked from 'package:grDevices': windows Loading required package: OrganismDbi Loading required package: GenomicFeatures Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: GO.db Loading required package: org.Hs.eg.db Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene Attaching package: 'GGtools' The following object is masked from 'package:stats': getCall > library(ff) Loading required package: bit Attaching package: 'bit' The following object is masked from 'package:data.table': setattr The following object is masked from 'package:base': xor Attaching package ff - getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpAV1VqX/ff" - getOption("ffextension")=="ff" - getOption("ffdrop")==TRUE - getOption("fffinonexit")==TRUE - getOption("ffpagesize")==65536 - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes - getOption("ffbatchbytes")==37570478.08 -- consider a different value for tuning your system - getOption("ffmaxbytes")==1878523904 -- consider a different value for tuning your system Attaching package: 'ff' The following objects are masked from 'package:utils': write.csv, write.csv2 The following objects are masked from 'package:base': is.factor, is.ordered > > tenOn2021 = + c( "GI_4557248-S", "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S", + "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S") > > c22 = getSS("GGdata", "22") > c22 = c22[probeId(tenOn2021),] > > e1 = eqtlTests(c22, ~1, targdir = "ooo") > m1 = meqtlTests(list(c22, c22), list(~1, ~1), targdir = "ooobb") > > ae = as.ram(e1@fffile) opening ff C:/Users/biocbuild/bbs-3.11-bioc/meat/GGtools.Rcheck/tests_i386/ooo/foo_chr22.ff > am = as.ram(m1@fffile) > all.equal(as.numeric(ae)*2 ,as.numeric(am) ) [1] TRUE > > system("rm -rf ooo") /usr/bin/rm: cannot remove 'ooo/foo_chr22.ff': Device or resource busy [1] 1 > system("rm -rf ooobb") /usr/bin/rm: cannot remove 'ooobb/mfoo_22_summ.ff': Device or resource busy /usr/bin/rm: cannot remove 'ooobb/mfoo_chr22.ff': Device or resource busy [1] 1 > > proc.time() user system elapsed 30.90 2.79 51.29 |
GGtools.Rcheck/tests_x64/test.meqtlTests.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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(GGtools) Loading required package: GGBase Loading required package: snpStats Loading required package: survival Loading required package: Matrix Loading required package: data.table Loading required package: parallel Loading required package: Homo.sapiens Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics 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 object is masked from 'package:Matrix': which 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: 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: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:data.table': first, second The following object is masked from 'package:Matrix': expand The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:data.table': shift The following object is masked from 'package:grDevices': windows Loading required package: OrganismDbi Loading required package: GenomicFeatures Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: GO.db Loading required package: org.Hs.eg.db Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene Attaching package: 'GGtools' The following object is masked from 'package:stats': getCall > library(ff) Loading required package: bit Attaching package: 'bit' The following object is masked from 'package:data.table': setattr The following object is masked from 'package:base': xor Attaching package ff - getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpK6fs8B/ff" - getOption("ffextension")=="ff" - getOption("ffdrop")==TRUE - getOption("fffinonexit")==TRUE - getOption("ffpagesize")==65536 - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes - getOption("ffbatchbytes")==685831618.56 -- consider a different value for tuning your system - getOption("ffmaxbytes")==34291580928 -- consider a different value for tuning your system Attaching package: 'ff' The following objects are masked from 'package:utils': write.csv, write.csv2 The following objects are masked from 'package:base': is.factor, is.ordered > > tenOn2021 = + c( "GI_4557248-S", "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S", + "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S") > > c22 = getSS("GGdata", "22") > c22 = c22[probeId(tenOn2021),] > > e1 = eqtlTests(c22, ~1, targdir = "ooo") > m1 = meqtlTests(list(c22, c22), list(~1, ~1), targdir = "ooobb") > > ae = as.ram(e1@fffile) opening ff C:/Users/biocbuild/bbs-3.11-bioc/meat/GGtools.Rcheck/tests_x64/ooo/foo_chr22.ff > am = as.ram(m1@fffile) > all.equal(as.numeric(ae)*2 ,as.numeric(am) ) [1] TRUE > > system("rm -rf ooo") /usr/bin/rm: cannot remove 'ooo/foo_chr22.ff': Device or resource busy [1] 1 > system("rm -rf ooobb") /usr/bin/rm: cannot remove 'ooobb/mfoo_22_summ.ff': Device or resource busy /usr/bin/rm: cannot remove 'ooobb/mfoo_chr22.ff': Device or resource busy [1] 1 > > proc.time() user system elapsed 29.81 1.76 35.87 |
GGtools.Rcheck/tests_i386/test.meta.trans.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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. > > heavyTest = function() { + library(GGtools) + + # verifies that transScores agrees with snp.rhs.tests to obtain best + # trans scores + + tenOn2021 = + c( "GI_4557248-S", "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S", + "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S") + + suppressPackageStartupMessages(library(GGtools)) + + mt1 = meta.transScores(c("GGdata", "GGdata"), rhs=list(~1, ~1), snpchr="22", chrnames=as.character(c(20,21)), + # + # all tests are trans, to verify buffering approach + # + radius = 2e+06, K=4, targdir="uiu2", + probesToKeep = tenOn2021, batchsize = 200, + geneannopk = "illuminaHumanv1.db", + snpannopk = "SNPlocs.Hsapiens.dbSNP.20111119", gchrpref = "", SMFilterList = list( function(x) x[probeId(tenOn2021),], + function(x) x[probeId(tenOn2021), ]), + schrpref = "ch", exFilter = list( function(x) x, function(x) x)) + + transTab(mt1) + } > > proc.time() user system elapsed 0.26 0.07 0.31 |
GGtools.Rcheck/tests_x64/test.meta.trans.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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. > > heavyTest = function() { + library(GGtools) + + # verifies that transScores agrees with snp.rhs.tests to obtain best + # trans scores + + tenOn2021 = + c( "GI_4557248-S", "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S", + "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S") + + suppressPackageStartupMessages(library(GGtools)) + + mt1 = meta.transScores(c("GGdata", "GGdata"), rhs=list(~1, ~1), snpchr="22", chrnames=as.character(c(20,21)), + # + # all tests are trans, to verify buffering approach + # + radius = 2e+06, K=4, targdir="uiu2", + probesToKeep = tenOn2021, batchsize = 200, + geneannopk = "illuminaHumanv1.db", + snpannopk = "SNPlocs.Hsapiens.dbSNP.20111119", gchrpref = "", SMFilterList = list( function(x) x[probeId(tenOn2021),], + function(x) x[probeId(tenOn2021), ]), + schrpref = "ch", exFilter = list( function(x) x, function(x) x)) + + transTab(mt1) + } > > proc.time() user system elapsed 0.21 0.06 0.26 |
GGtools.Rcheck/tests_i386/testCisMap.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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. > if (.Platform$OS.type != "windows") { + t20 = GGtools:::getCisMap() + + NL = GGtools:::namelist(t20) + + NL1 = NL[[1]] + + t20sl = t20@snplocs[NL1] + + probe1 = names(NL)[1] + + TARG = t20@generanges[probe1]-50000 + + d = distance(TARG, t20sl) + + all(d <= 50000) + } else TRUE [1] TRUE > > proc.time() user system elapsed 0.28 0.04 0.31 |
GGtools.Rcheck/tests_x64/testCisMap.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (.Platform$OS.type != "windows") { + t20 = GGtools:::getCisMap() + + NL = GGtools:::namelist(t20) + + NL1 = NL[[1]] + + t20sl = t20@snplocs[NL1] + + probe1 = names(NL)[1] + + TARG = t20@generanges[probe1]-50000 + + d = distance(TARG, t20sl) + + all(d <= 50000) + } else TRUE [1] TRUE > > proc.time() user system elapsed 0.29 0.04 0.62 |
GGtools.Rcheck/tests_i386/testTrans.Rout.fail R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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. > # verifies that transScores agrees with snp.rhs.tests to obtain best > # trans scores > > suppressPackageStartupMessages(library(GGtools)) > > tenOn2021 = + c( "GI_4557248-S", "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S", + "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S") > > tconf = new("TransConfig") > radius(tconf) = 2000000L > smpack(tconf) = "GGdata" > rhs(tconf) = ~1 > snpchr(tconf) = "22" # we get scores for all SNP on this chrom > chrnames(tconf) = c("20", "21") > gbufsize(tconf) = 4L > smFilter(tconf) = function(x) x[probeId(tenOn2021),] > snpannopk(tconf) = snplocsDefault() > schrpref(tconf) = "ch" > exFilter(tconf) = function(x)x > gchrpref = "" > batchsize(tconf) = 200L > > suppressPackageStartupMessages(library(GGtools)) > > t1 = transScores(tconf) Loading required package: illuminaHumanv1.db opening ff C:/Users/biocbuild/bbs-3.11-bioc/meat/GGtools.Rcheck/tests_i386/cisScratch22/tsc_20_chr22.ff 2opening ff C:/Users/biocbuild/bbs-3.11-bioc/meat/GGtools.Rcheck/tests_i386/cisScratch22/tsctmp2_chr22.ff Error in get(".rambytes") : object '.rambytes' not found Calls: transScores -> updateKfeats -> chunk -> chunk.default -> get Execution halted |
GGtools.Rcheck/tests_x64/testTrans.Rout.fail R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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. > # verifies that transScores agrees with snp.rhs.tests to obtain best > # trans scores > > suppressPackageStartupMessages(library(GGtools)) > > tenOn2021 = + c( "GI_4557248-S", "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S", + "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S") > > tconf = new("TransConfig") > radius(tconf) = 2000000L > smpack(tconf) = "GGdata" > rhs(tconf) = ~1 > snpchr(tconf) = "22" # we get scores for all SNP on this chrom > chrnames(tconf) = c("20", "21") > gbufsize(tconf) = 4L > smFilter(tconf) = function(x) x[probeId(tenOn2021),] > snpannopk(tconf) = snplocsDefault() > schrpref(tconf) = "ch" > exFilter(tconf) = function(x)x > gchrpref = "" > batchsize(tconf) = 200L > > suppressPackageStartupMessages(library(GGtools)) > > t1 = transScores(tconf) Loading required package: illuminaHumanv1.db opening ff C:/Users/biocbuild/bbs-3.11-bioc/meat/GGtools.Rcheck/tests_x64/cisScratch22/tsc_20_chr22.ff 2opening ff C:/Users/biocbuild/bbs-3.11-bioc/meat/GGtools.Rcheck/tests_x64/cisScratch22/tsctmp2_chr22.ff Error in get(".rambytes") : object '.rambytes' not found Calls: transScores -> updateKfeats -> chunk -> chunk.default -> get Execution halted |
GGtools.Rcheck/examples_i386/GGtools-Ex.timings
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GGtools.Rcheck/examples_x64/GGtools-Ex.timings
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