Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:25:10 -0400 (Thu, 12 Apr 2018).
Package 502/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
focalCall 1.12.0 Oscar Krijgsman
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: focalCall |
Version: 1.12.0 |
Command: rm -rf focalCall.buildbin-libdir focalCall.Rcheck && mkdir focalCall.buildbin-libdir focalCall.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=focalCall.buildbin-libdir focalCall_1.12.0.tar.gz >focalCall.Rcheck\00install.out 2>&1 && cp focalCall.Rcheck\00install.out focalCall-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=focalCall.buildbin-libdir --install="check:focalCall-install.out" --force-multiarch --no-vignettes --timings focalCall_1.12.0.tar.gz |
StartedAt: 2018-04-12 00:04:26 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 00:05:47 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 80.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: focalCall.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf focalCall.buildbin-libdir focalCall.Rcheck && mkdir focalCall.buildbin-libdir focalCall.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=focalCall.buildbin-libdir focalCall_1.12.0.tar.gz >focalCall.Rcheck\00install.out 2>&1 && cp focalCall.Rcheck\00install.out focalCall-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=focalCall.buildbin-libdir --install="check:focalCall-install.out" --force-multiarch --no-vignettes --timings focalCall_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/focalCall.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'focalCall/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'focalCall' version '1.12.0' * 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 'focalCall' can be installed ... OK * 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 ** checking loading without being on the library search path ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK ** checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .match_CNV2CGH: no visible global function definition for 'bpstart' .match_CNV2CGH: no visible global function definition for 'chromosomes' .match_CNV2CGH: no visible global function definition for 'bpend' FreqPlot: no visible global function definition for 'chromosomes' FreqPlot: no visible global function definition for 'plot' FreqPlot: no visible global function definition for 'points' FreqPlot: no visible global function definition for 'abline' FreqPlot: no visible global function definition for 'axis' FreqPlotfocal: no visible global function definition for 'chromosomes' FreqPlotfocal: no visible global function definition for 'assayDataElement' FreqPlotfocal: no visible global function definition for 'fData' FreqPlotfocal: no visible global function definition for 'plot' FreqPlotfocal: no visible global function definition for 'points' FreqPlotfocal: no visible global function definition for 'abline' FreqPlotfocal: no visible global function definition for 'axis' focalCall: no visible global function definition for 'calls' focalCall: no visible global function definition for 'featureNames' focalCall: no visible global function definition for 'segmented' focalCall: no visible global function definition for 'chromosomes' focalCall: no visible global function definition for 'bpstart' focalCall: no visible global function definition for 'assayDataElement<-' focalCall: no visible global function definition for 'assayDataElement' focalCall: no visible global function definition for 'bpend' focalCall: no visible global function definition for 'fData' focalCall: no visible global function definition for 'fData<-' focalCall: no visible global function definition for 'write.table' igvFiles: no visible global function definition for 'calls' igvFiles: no visible global function definition for 'chromosomes' igvFiles: no visible global function definition for 'bpstart' igvFiles: no visible global function definition for 'bpend' igvFiles: no visible global function definition for 'featureNames' igvFiles: no visible global function definition for 'segmented' igvFiles: no visible global function definition for 'write.table' igvFiles: no visible global function definition for 'assayDataElement' singleSample: no visible global function definition for 'calls' singleSample: no visible global function definition for 'featureNames' singleSample: no visible global function definition for 'fData' singleSample: no visible global function definition for 'fData<-' singleSample: no visible global function definition for 'assayDataElement<-' singleSample: no visible global function definition for 'segmented' singleSample: no visible global function definition for 'chromosomes' singleSample: no visible global function definition for 'bpend' singleSample: no visible global function definition for 'bpstart' singleSample: no visible global function definition for 'assayDataElement' singleSample: no visible global function definition for 'median' singleSample: no visible global function definition for 'png' singleSample: no visible global function definition for 'plot' singleSample: no visible global function definition for 'dev.off' singleSample: no visible global function definition for 'write.table' Undefined global functions or variables: abline assayDataElement assayDataElement<- axis bpend bpstart calls chromosomes dev.off fData fData<- featureNames median plot png points segmented write.table Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "abline", "axis", "plot", "points") importFrom("stats", "median") importFrom("utils", "write.table") 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/focalCall.Rcheck/00check.log' for details.
focalCall.Rcheck/00install.out
install for i386 * installing *source* package 'focalCall' ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'focalCall' finding HTML links ... done BierkensCNA html FreqPlot html FreqPlotfocal html focalCall html igvFiles html singleSample html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'focalCall' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'focalCall' as focalCall_1.12.0.zip * DONE (focalCall) In R CMD INSTALL In R CMD INSTALL
focalCall.Rcheck/tests_i386/runTests.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("focalCall") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Attaching package: 'snow' The following objects are masked from 'package:BiocGenerics': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, parApply, parCapply, parLapply, parRapply, parSapply The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, makeCluster, parApply, parCapply, parLapply, parRapply, parSapply, splitIndices, stopCluster Attaching package: 'CGHcall' The following object is masked from 'package:BiocGenerics': normalize RUNIT TEST PROTOCOL -- Thu Apr 12 00:05:42 2018 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : focalCall RUnit Tests - 0 test functions, 0 errors, 0 failures Number of test functions: 0 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 0.96 0.03 1.00 |
focalCall.Rcheck/tests_x64/runTests.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("focalCall") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Attaching package: 'snow' The following objects are masked from 'package:BiocGenerics': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, parApply, parCapply, parLapply, parRapply, parSapply The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, makeCluster, parApply, parCapply, parLapply, parRapply, parSapply, splitIndices, stopCluster Attaching package: 'CGHcall' The following object is masked from 'package:BiocGenerics': normalize RUNIT TEST PROTOCOL -- Thu Apr 12 00:05:44 2018 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : focalCall RUnit Tests - 0 test functions, 0 errors, 0 failures Number of test functions: 0 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 1.15 0.04 1.20 |
focalCall.Rcheck/examples_i386/focalCall-Ex.timings
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focalCall.Rcheck/examples_x64/focalCall-Ex.timings
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