Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:32:55 -0400 (Wed, 16 Oct 2019).
Package 447/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
DMRcaller 1.16.0 Nicolae Radu Zabet
| 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: DMRcaller |
Version: 1.16.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRcaller.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DMRcaller_1.16.0.tar.gz |
StartedAt: 2019-10-16 03:17:51 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 03:25:41 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 470.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DMRcaller.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRcaller.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DMRcaller_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DMRcaller.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 'DMRcaller/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'DMRcaller' version '1.16.0' * 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 ... OK * checking for portable file names ... OK * checking whether package 'DMRcaller' can be installed ... OK * 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 * 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 ... NOTE extractGC: no visible global function definition for 'getSeq' extractGC: no visible global function definition for 'seqlevels' Undefined global functions or variables: getSeq seqlevels * 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 Examples with CPU or elapsed time > 5s user system elapsed readBismarkPool 8.10 0.10 8.20 mergeDMRsIteratively 7.61 0.00 7.66 computeDMRs 5.67 0.06 5.74 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed readBismarkPool 8.50 0.36 8.86 mergeDMRsIteratively 6.98 0.03 7.02 computeDMRs 6.40 0.16 6.56 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.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 NOTE See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DMRcaller.Rcheck/00check.log' for details.
DMRcaller.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DMRcaller_1.16.0.tar.gz && rm -rf DMRcaller.buildbin-libdir && mkdir DMRcaller.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DMRcaller.buildbin-libdir DMRcaller_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DMRcaller_1.16.0.zip && rm DMRcaller_1.16.0.tar.gz DMRcaller_1.16.0.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 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1127k 100 1127k 0 0 15.9M 0 --:--:-- --:--:-- --:--:-- 17.4M install for i386 * installing *source* package 'DMRcaller' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'DMRcaller' finding HTML links ... done DMRcaller html finding level-2 HTML links ... done DMRsNoiseFilterCG html GEs html analyseReadsInsideRegionsForCondition html computeDMRs html computeDMRsReplicates html computeMethylationDataCoverage html computeMethylationDataSpatialCorrelation html computeMethylationProfile html computeOverlapProfile html extractGC html filterDMRs html getWholeChromosomes html joinReplicates html mergeDMRsIteratively html methylationDataList html plotLocalMethylationProfile html plotMethylationDataCoverage html plotMethylationDataSpatialCorrelation html plotMethylationProfile html plotMethylationProfileFromData html plotOverlapProfile html poolMethylationDatasets html poolTwoMethylationDatasets html readBismark html readBismarkPool html saveBismark html syntheticDataReplicates 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 'DMRcaller' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'DMRcaller' as DMRcaller_1.16.0.zip * DONE (DMRcaller) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'DMRcaller' successfully unpacked and MD5 sums checked
DMRcaller.Rcheck/tests_i386/runTests.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. > BiocGenerics:::testPackage("DMRcaller") 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 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Parameters checking ... Extract methylation in the corresponding context Computing DMRs Merge adjacent DMRs Merge DMRs iteratively Filter DMRs Parameters checking ... Extract methylation in the corresponding context Computing DMRs at Chr1:1..4976 Calculating interpolations... Identifying DMRs... Analysed reads inside DMRs Merge DMRs iteratively Filter DMRs Parameters checking ... Extract methylation in the corresponding context Computing DMRs at Chr1:1..4976 Selecting data... Identifying DMRs... Validating objects Finding overlaps Joining objects Parameters checking ... Extract methylation in the corresponding context Computing DMRs at Chr1:1..4976 Count inside each bin... Filter the bins... Identifying DMRs... Merge adjacent DMRs Merge DMRs iteratively Filter DMRs Parameters checking ... Merge DMRs iteratively ... RUNIT TEST PROTOCOL -- Wed Oct 16 03:23:30 2019 *********************************************** Number of test functions: 6 Number of errors: 0 Number of failures: 0 1 Test Suite : DMRcaller RUnit Tests - 6 test functions, 0 errors, 0 failures Number of test functions: 6 Number of errors: 0 Number of failures: 0 Warning message: In fisher.test(matrix(unlist(x), nrow = 2, byrow = TRUE), alternative = alternative) : 'x' has been rounded to integer: Mean relative difference: 0.002857143 > > proc.time() user system elapsed 125.35 0.57 125.93 |
DMRcaller.Rcheck/tests_x64/runTests.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. > BiocGenerics:::testPackage("DMRcaller") 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 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Parameters checking ... Extract methylation in the corresponding context Computing DMRs Merge adjacent DMRs Merge DMRs iteratively Filter DMRs Parameters checking ... Extract methylation in the corresponding context Computing DMRs at Chr1:1..4976 Calculating interpolations... Identifying DMRs... Analysed reads inside DMRs Merge DMRs iteratively Filter DMRs Parameters checking ... Extract methylation in the corresponding context Computing DMRs at Chr1:1..4976 Selecting data... Identifying DMRs... Validating objects Finding overlaps Joining objects Parameters checking ... Extract methylation in the corresponding context Computing DMRs at Chr1:1..4976 Count inside each bin... Filter the bins... Identifying DMRs... Merge adjacent DMRs Merge DMRs iteratively Filter DMRs Parameters checking ... Merge DMRs iteratively ... RUNIT TEST PROTOCOL -- Wed Oct 16 03:25:29 2019 *********************************************** Number of test functions: 6 Number of errors: 0 Number of failures: 0 1 Test Suite : DMRcaller RUnit Tests - 6 test functions, 0 errors, 0 failures Number of test functions: 6 Number of errors: 0 Number of failures: 0 Warning message: In fisher.test(matrix(unlist(x), nrow = 2, byrow = TRUE), alternative = alternative) : 'x' has been rounded to integer: Mean relative difference: 0.002857143 > > proc.time() user system elapsed 118.37 0.51 118.87 |
DMRcaller.Rcheck/examples_i386/DMRcaller-Ex.timings
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DMRcaller.Rcheck/examples_x64/DMRcaller-Ex.timings
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