Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:34:19 -0400 (Wed, 16 Oct 2019).
Package 393/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
DChIPRep 1.14.0 Bernd Klaus
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: DChIPRep |
Version: 1.14.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DChIPRep.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DChIPRep_1.14.0.tar.gz |
StartedAt: 2019-10-16 03:04:43 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 03:15:24 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 640.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DChIPRep.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DChIPRep.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DChIPRep_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DChIPRep.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 'DChIPRep/DESCRIPTION' ... OK * this is package 'DChIPRep' version '1.14.0' * 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 'DChIPRep' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:36: file link 'regionPlot' in package 'soGGi' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:14: file link 'GenomicRanges-class' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:27: file link 'regionPlot' in package 'soGGi' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:65: file link 'regionPlot' in package 'soGGi' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/robust_mean.Rd:17: file link 'smhuber' in package 'smoothmest' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DChIPRep.Rcheck/00install.out' for details. * checking installed package size ... OK * 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 ... 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 Examples with CPU or elapsed time > 5s user system elapsed importData 7.94 0.03 8.22 plotProfiles 6.10 0.20 6.29 plotSignificance 6.09 0.08 6.17 FDRresults 3.98 1.08 5.06 show 3.53 0.02 8.14 summarizeCountsPerPosition 2.66 0.01 5.48 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed plotSignificance 6.86 0.04 6.90 plotProfiles 6.55 0.10 6.64 * 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: 1 WARNING, 1 NOTE See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DChIPRep.Rcheck/00check.log' for details.
DChIPRep.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DChIPRep_1.14.0.tar.gz && rm -rf DChIPRep.buildbin-libdir && mkdir DChIPRep.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DChIPRep.buildbin-libdir DChIPRep_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DChIPRep_1.14.0.zip && rm DChIPRep_1.14.0.tar.gz DChIPRep_1.14.0.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 690k 100 690k 0 0 9104k 0 --:--:-- --:--:-- --:--:-- 9.7M install for i386 * installing *source* package 'DChIPRep' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** exec ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'DChIPRep' finding HTML links ... done DChIPRep html DChIPRepResults html DESeq2Data html FDRresults html TSS_galonska html chip_galonska html exampleChipData html exampleInputData html exampleSampleTable html getMATfromDataFrame html importData html importDataFromMatrices html importData_soGGi html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:36: file link 'regionPlot' in package 'soGGi' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:14: file link 'GenomicRanges-class' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:27: file link 'regionPlot' in package 'soGGi' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:65: file link 'regionPlot' in package 'soGGi' does not exist and so has been treated as a topic input_galonska html plotProfiles html plotSignificance html resultsDChIPRep html robust_mean html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/robust_mean.Rd:17: file link 'smhuber' in package 'smoothmest' does not exist and so has been treated as a topic runTesting html sample_table_galonska html show html summarizeCountsPerPosition html testData 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 'DChIPRep' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'DChIPRep' as DChIPRep_1.14.0.zip * DONE (DChIPRep) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'DChIPRep' successfully unpacked and MD5 sums checked
DChIPRep.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) > library(DChIPRep) Loading required package: DESeq2 Loading required package: S4Vectors 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 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: GenomicRanges 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 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 > > test_check("DChIPRep") Step 1... determine cutoff point Step 2... estimate parameters of null distribution and eta0 Step 3... compute p-values and estimate empirical PDF/CDF Step 4... compute q-values and local fdr Step 1... determine cutoff point Step 2... estimate parameters of null distribution and eta0 Step 3... compute p-values and estimate empirical PDF/CDF Step 4... compute q-values and local fdr Step 1... determine cutoff point Step 2... estimate parameters of null distribution and eta0 Step 3... compute p-values and estimate empirical PDF/CDF Step 4... compute q-values and local fdr Step 1... determine cutoff point Step 2... estimate parameters of null distribution and eta0 Step 3... compute p-values and estimate empirical PDF/CDF Step 4... compute q-values and local fdr == testthat results =========================================================== [ OK: 19 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ] > > > # code for checking and saving the log > ## ff <- file("check.out", open = "wt") > ## sink(file = ff, type = "message") > ## sink(type = "message") > ## sink() > > > > proc.time() user system elapsed 33.23 2.03 35.32 |
DChIPRep.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) > library(DChIPRep) Loading required package: DESeq2 Loading required package: S4Vectors 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 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: GenomicRanges 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 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 > > test_check("DChIPRep") Step 1... determine cutoff point Step 2... estimate parameters of null distribution and eta0 Step 3... compute p-values and estimate empirical PDF/CDF Step 4... compute q-values and local fdr Step 1... determine cutoff point Step 2... estimate parameters of null distribution and eta0 Step 3... compute p-values and estimate empirical PDF/CDF Step 4... compute q-values and local fdr Step 1... determine cutoff point Step 2... estimate parameters of null distribution and eta0 Step 3... compute p-values and estimate empirical PDF/CDF Step 4... compute q-values and local fdr Step 1... determine cutoff point Step 2... estimate parameters of null distribution and eta0 Step 3... compute p-values and estimate empirical PDF/CDF Step 4... compute q-values and local fdr == testthat results =========================================================== [ OK: 19 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ] > > > # code for checking and saving the log > ## ff <- file("check.out", open = "wt") > ## sink(file = ff, type = "message") > ## sink(type = "message") > ## sink() > > > > proc.time() user system elapsed 33.12 0.78 33.89 |
DChIPRep.Rcheck/examples_i386/DChIPRep-Ex.timings
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DChIPRep.Rcheck/examples_x64/DChIPRep-Ex.timings
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