Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:36:21 -0400 (Wed, 17 Oct 2018).
Package 1153/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
PWMEnrich 4.16.0 Robert Stojnic
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: PWMEnrich |
Version: 4.16.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PWMEnrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings PWMEnrich_4.16.0.tar.gz |
StartedAt: 2018-10-17 04:08:05 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 04:11:04 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 179.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PWMEnrich.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PWMEnrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings PWMEnrich_4.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/PWMEnrich.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'PWMEnrich/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PWMEnrich' version '4.16.0' * 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 'PWMEnrich' 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 ... NOTE 'library' or 'require' calls in package code: 'PWMEnrich.Dmelanogaster.background' 'PWMEnrich.Hsapiens.background' 'PWMEnrich.Mmusculus.background' 'parallel' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE colMedians: no visible binding for global variable 'median' getPromoters: no visible global function definition for 'providerVersion' getPromoters: no visible global function definition for 'data' gevPerSequence: no visible global function definition for 'predict.lm' logNormPval: no visible global function definition for 'plnorm' makePWMGEVBackground : <anonymous>: no visible global function definition for 'lm' makePWMLognBackground : dlnorm.lcen: no visible global function definition for 'dlnorm' makePWMLognBackground : dlnorm.lcen: no visible global function definition for 'plnorm' makePWMLognBackground: no visible global function definition for 'quantile' makePWMLognBackground: no visible global function definition for 'median' makePWMLognBackground: no visible global function definition for 'optimize' makePWMPvalCutoffBackground: no visible global function definition for 'quantile' makePWMPvalCutoffBackground: no visible global function definition for 'ecdf' makePWMPvalCutoffBackgroundFromSeq: no visible global function definition for 'na.omit' makePWMPvalCutoffBackgroundFromSeq: no visible global function definition for 'quantile' makePWMPvalCutoffBackgroundFromSeq: no visible global function definition for 'ecdf' motifEcdf : <anonymous>: no visible global function definition for 'na.omit' motifEcdf: no visible binding for global variable 'ecdf' motifEnrichment: no visible binding for global variable 'qlnorm' motifEnrichment : <anonymous>: no visible global function definition for 'pchisq' motifScores: no visible global function definition for 'mclapply' motifScoresBigMemory: no visible global function definition for 'mclapply' plotMotifScores: no visible global function definition for 'palette' plotMotifScores: no visible global function definition for 'col2rgb' plotMotifScores: no visible global function definition for 'rgb' plotMotifScores: no visible global function definition for 'par' plotMotifScores: no visible global function definition for 'lines' plotMotifScores: no visible global function definition for 'polygon' plotMotifScores: no visible global function definition for 'rect' plotMotifScores: no visible global function definition for 'text' registerCoresPWMEnrich: no visible global function definition for 'detectCores' tryAllMotifAlignments : <anonymous>: no visible global function definition for 'cor' Undefined global functions or variables: col2rgb cor data detectCores dlnorm ecdf lines lm mclapply median na.omit optimize palette par pchisq plnorm polygon predict.lm providerVersion qlnorm quantile rect rgb text Consider adding importFrom("grDevices", "col2rgb", "palette", "rgb") importFrom("graphics", "lines", "par", "polygon", "rect", "text") importFrom("stats", "cor", "dlnorm", "ecdf", "lm", "median", "na.omit", "optimize", "pchisq", "plnorm", "predict.lm", "qlnorm", "quantile") importFrom("utils", "data") to your NAMESPACE file. * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running '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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/PWMEnrich.Rcheck/00check.log' for details.
PWMEnrich.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/PWMEnrich_4.16.0.tar.gz && rm -rf PWMEnrich.buildbin-libdir && mkdir PWMEnrich.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PWMEnrich.buildbin-libdir PWMEnrich_4.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL PWMEnrich_4.16.0.zip && rm PWMEnrich_4.16.0.tar.gz PWMEnrich_4.16.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 3482k 100 3482k 0 0 31.8M 0 --:--:-- --:--:-- --:--:-- 34.0M install for i386 * installing *source* package 'PWMEnrich' ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'PWMEnrich' finding HTML links ... done MotifEnrichmentReport html MotifEnrichmentResults html PFMtoPWM html PWM html PWMCutoffBackground html PWMEmpiricalBackground html PWMGEVBackground html PWMLognBackground html PWMUnscaled html as.data.frame-commaMotifEnrichmentReport-method html getBackgroundFrequencies html groupReport-commaMotifEnrichmentResults-method html makeBackground html makePWMCutoffBackground html makePWMEmpiricalBackground html makePWMGEVBackground html makePWMLognBackground html makePWMPvalCutoffBackground html makePWMPvalCutoffBackgroundFromSeq html makePriors html motifDiffEnrichment html motifEcdf html motifEnrichment html motifIC html motifRankingForGroup-commaMotifEnrichmentResults-method html motifRankingForSequence-commaMotifEnrichmentResults-method html motifScores html motifSimilarity html operators-MotifEnrichmentReport html operators-MotifEnrichmentResults html operators-PWM html operators-PWMCutoffBackground html operators-PWMEmpiricalBackground html operators-PWMGEVBackground html operators-PWMLognBackground html plot html plotMotifScores html plotMultipleMotifs html plotTopMotifsGroup-commaMotifEnrichmentResults-method html plotTopMotifsSequence-commaMotifEnrichmentResults-method html readMotifs html registerCoresPWMEnrich html reverseComplement html scanWithPWM html seqLogoGrid html sequenceReport-commaMotifEnrichmentResults-method html subsetting-PWMCutoffBackground html subsetting-PWMEmpiricalBackground html subsetting-PWMGEVBackground html subsetting-PWMLognBackground html toPWM html useBigMemoryPWMEnrich html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'PWMEnrich' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'PWMEnrich' as PWMEnrich_4.16.0.zip * DONE (PWMEnrich) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'PWMEnrich' successfully unpacked and MD5 sums checked In R CMD INSTALL
PWMEnrich.Rcheck/tests_i386/test-all.Rout R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray" 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) > library(PWMEnrich) Loading required package: grid 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, colMeans, colSums, colnames, dirname, 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: Biostrings Loading required package: S4Vectors Loading required package: stats4 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: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit > > test_package("PWMEnrich") Calculating motif enrichment scores ... Calculating motif enrichment scores ... NOTE: Using the 'default' algorithm to infer background parameters, appropriate for all organisms except human. Calculating motif enrichment scores ... Calculating motif enrichment scores ... Calculating motif enrichment scores ... Calculating motif enrichment scores ... Calculating motif enrichment scores ... Calculating motif enrichment scores ... Calculating motif enrichment scores ... Calculating motif enrichment scores ... NOTE: Using the 'default' algorithm to infer background parameters, appropriate for all organisms except human. Calculating motif enrichment scores ... Calculating motif enrichment scores ... == testthat results =========================================================== OK: 48 SKIPPED: 0 FAILED: 0 Warning message: Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead > > > proc.time() user system elapsed 4.31 0.20 5.21 |
PWMEnrich.Rcheck/tests_x64/test-all.Rout R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray" 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) > library(PWMEnrich) Loading required package: grid 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, colMeans, colSums, colnames, dirname, 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: Biostrings Loading required package: S4Vectors Loading required package: stats4 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: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit > > test_package("PWMEnrich") Calculating motif enrichment scores ... Calculating motif enrichment scores ... NOTE: Using the 'default' algorithm to infer background parameters, appropriate for all organisms except human. Calculating motif enrichment scores ... Calculating motif enrichment scores ... Calculating motif enrichment scores ... Calculating motif enrichment scores ... Calculating motif enrichment scores ... Calculating motif enrichment scores ... Calculating motif enrichment scores ... Calculating motif enrichment scores ... NOTE: Using the 'default' algorithm to infer background parameters, appropriate for all organisms except human. Calculating motif enrichment scores ... Calculating motif enrichment scores ... == testthat results =========================================================== OK: 48 SKIPPED: 0 FAILED: 0 Warning message: Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead > > > proc.time() user system elapsed 5.85 0.21 6.06 |
PWMEnrich.Rcheck/examples_i386/PWMEnrich-Ex.timings
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PWMEnrich.Rcheck/examples_x64/PWMEnrich-Ex.timings
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