Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:26:09 -0400 (Thu, 12 Apr 2018).
Package 1322/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
soGGi 1.10.0 Tom Carroll
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | ![]() |
Package: soGGi |
Version: 1.10.0 |
Command: rm -rf soGGi.buildbin-libdir soGGi.Rcheck && mkdir soGGi.buildbin-libdir soGGi.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=soGGi.buildbin-libdir soGGi_1.10.0.tar.gz >soGGi.Rcheck\00install.out 2>&1 && cp soGGi.Rcheck\00install.out soGGi-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=soGGi.buildbin-libdir --install="check:soGGi-install.out" --force-multiarch --no-vignettes --timings soGGi_1.10.0.tar.gz |
StartedAt: 2018-04-12 03:18:38 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 03:24:16 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 337.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: soGGi.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf soGGi.buildbin-libdir soGGi.Rcheck && mkdir soGGi.buildbin-libdir soGGi.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=soGGi.buildbin-libdir soGGi_1.10.0.tar.gz >soGGi.Rcheck\00install.out 2>&1 && cp soGGi.Rcheck\00install.out soGGi-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=soGGi.buildbin-libdir --install="check:soGGi-install.out" --force-multiarch --no-vignettes --timings soGGi_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/soGGi.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 'soGGi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'soGGi' version '1.10.0' * 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 'soGGi' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/soGGi.Rcheck/00install.out' for details. * 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 ... NOTE Foreign function call to a different package: .Call("rle_sum_any", ..., PACKAGE = "chipseq") See chapter 'System and foreign language interfaces' in the 'Writing R Extensions' manual. * checking R code for possible problems ... NOTE GetGRanges: no visible global function definition for 'read.delim' GetGRanges: possible error in `seqlevels<-`(RegionRanges, force = TRUE, value = `*tmpv*`): unused argument (force = TRUE) findconsensusRegions : <anonymous>: no visible global function definition for 'weighted.mean' getShifts: no visible global function definition for 'readGAlignmentsFromBam' getSummitScore: no visible global function definition for 'readGAlignmentsFromBam' plotRegion.ChIPprofile: no visible global function definition for 'formula' runFindSummit: no visible global function definition for 'readGAlignmentsFromBam' runRegionPlot : <anonymous>: no visible global function definition for 'spline' summitPipeline: no visible global function definition for 'readGAlignmentsFromBam' plotRegion,ChIPprofile: no visible global function definition for 'formula' Undefined global functions or variables: formula read.delim readGAlignmentsFromBam spline weighted.mean Consider adding importFrom("stats", "formula", "spline", "weighted.mean") importFrom("utils", "read.delim") 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 ... WARNING Codoc mismatches from documentation object 'c,ChIPprofile-method': \S4method{c}{ChIPprofile} Code: function(x, ...) Docs: function(x, ..., recursive = FALSE) Argument names in docs not in code: recursive * 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 '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: 2 WARNINGs, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/soGGi.Rcheck/00check.log' for details.
soGGi.Rcheck/00install.out
install for i386 * installing *source* package 'soGGi' ... ** R ** data ** inst ** preparing package for lazy loading Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi' ** help *** installing help indices converting help for package 'soGGi' finding HTML links ... done ChIPprofile html Ops html chipExampleBig html findconsensusRegions html groupByOverlaps html ik_Example html ik_Profiles html manipulateObjects html normalise html normaliseQuantiles html orientBy html plotRegion html pwmCov html pwmToCoverage html singleGRange html ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi' In R CMD INSTALL install for x64 * installing *source* package 'soGGi' ... ** testing if installed package can be loaded Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi' * MD5 sums packaged installation of 'soGGi' as soGGi_1.10.0.zip * DONE (soGGi) In R CMD INSTALL In R CMD INSTALL
soGGi.Rcheck/tests_i386/testthat.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. > library(testthat) > library(soGGi) 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, 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 Loading required package: SummarizedExperiment Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb 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 Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following object is masked from 'package:base': apply Warning message: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi' > > test_check("soGGi") == testthat results =========================================================== OK: 4 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 10.53 0.29 10.81 |
soGGi.Rcheck/tests_x64/testthat.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. > library(testthat) > library(soGGi) 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, 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 Loading required package: SummarizedExperiment Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb 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 Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following object is masked from 'package:base': apply Warning message: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi' > > test_check("soGGi") == testthat results =========================================================== OK: 4 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 11.39 0.31 11.70 |
soGGi.Rcheck/examples_i386/soGGi-Ex.timings
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soGGi.Rcheck/examples_x64/soGGi-Ex.timings
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