Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:44:49 -0400 (Wed, 17 Oct 2018).
Package 1492/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
topdownr 1.2.0 Sebastian Gibb
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: topdownr |
Version: 1.2.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:topdownr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings topdownr_1.2.0.tar.gz |
StartedAt: 2018-10-17 05:13:45 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 05:19:05 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 320.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: topdownr.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:topdownr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings topdownr_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/topdownr.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 'topdownr/DESCRIPTION' ... OK * this is package 'topdownr' version '1.2.0' * package encoding: UTF-8 * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'topdownr' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/AbstractTopDownSet-class.Rd:228: file link 'XStringViews' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/FragmentViews-class.Rd:75: file link 'AAString' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:27: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:48: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:49: file link 'defaultNeutralLoss' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:108: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:134: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:135: file link 'defaultNeutralLoss' in package 'MSnbase' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/topdownr.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 ... 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... 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: 1 WARNING, 1 NOTE See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/topdownr.Rcheck/00check.log' for details.
topdownr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/topdownr_1.2.0.tar.gz && rm -rf topdownr.buildbin-libdir && mkdir topdownr.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=topdownr.buildbin-libdir topdownr_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL topdownr_1.2.0.zip && rm topdownr_1.2.0.tar.gz topdownr_1.2.0.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 1889k 100 1889k 0 0 27.0M 0 --:--:-- --:--:-- --:--:-- 29.7M install for i386 * installing *source* package 'topdownr' ... ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'topdownr' finding HTML links ... done AbstractTopDownSet-class html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/AbstractTopDownSet-class.Rd:228: file link 'XStringViews' in package 'Biostrings' does not exist and so has been treated as a topic FragmentViews-class html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/FragmentViews-class.Rd:75: file link 'AAString' in package 'Biostrings' does not exist and so has been treated as a topic NCBSet-class html TopDownSet-class html default-functions html readTopDownFiles html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:27: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:48: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:49: file link 'defaultNeutralLoss' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:108: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:134: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:135: file link 'defaultNeutralLoss' in package 'MSnbase' does not exist and so has been treated as a topic tds html topdownr-package html windows-specific-functions html writeMethodXmls html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'topdownr' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'topdownr' as topdownr_1.2.0.zip * DONE (topdownr) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'topdownr' successfully unpacked and MD5 sums checked In R CMD INSTALL
topdownr.Rcheck/tests_i386/testthat.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("topdownr") 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: ProtGenerics 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 This is topdownr version 1.2.0 Visit https://sgibb.github.io/topdownr/ to get started. > > test_check("topdownr") == testthat results =========================================================== OK: 550 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 22.29 2.06 25.62 |
topdownr.Rcheck/tests_x64/testthat.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("topdownr") 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: ProtGenerics 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 This is topdownr version 1.2.0 Visit https://sgibb.github.io/topdownr/ to get started. > > test_check("topdownr") == testthat results =========================================================== OK: 550 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 24.53 1.21 26.42 |
topdownr.Rcheck/examples_i386/topdownr-Ex.timings
|
topdownr.Rcheck/examples_x64/topdownr-Ex.timings
|