Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:34:13 -0400 (Wed, 16 Oct 2019).
Package 963/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
metagenomeFeatures 2.4.0 Nathan D. Olson
| 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: metagenomeFeatures |
Version: 2.4.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagenomeFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings metagenomeFeatures_2.4.0.tar.gz |
StartedAt: 2019-10-16 05:04:44 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 05:07:13 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 149.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: metagenomeFeatures.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagenomeFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings metagenomeFeatures_2.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeFeatures.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 'metagenomeFeatures/DESCRIPTION' ... OK * this is package 'metagenomeFeatures' version '2.4.0' * 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 ... OK * checking for portable file names ... OK * checking whether package 'metagenomeFeatures' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpeYRn7d/R.INSTALLd7449897af/metagenomeFeatures/man/mgFeatures-class.Rd:27: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpeYRn7d/R.INSTALLd7449897af/metagenomeFeatures/man/reexports.Rd:14: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeFeatures.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: extdata 3.5Mb * 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 Package in Depends field not imported from: 'Biobase' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .select.taxa: no visible binding for global variable 'Keys' Undefined global functions or variables: Keys * 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 ** 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, 3 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeFeatures.Rcheck/00check.log' for details.
metagenomeFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/metagenomeFeatures_2.4.0.tar.gz && rm -rf metagenomeFeatures.buildbin-libdir && mkdir metagenomeFeatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metagenomeFeatures.buildbin-libdir metagenomeFeatures_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL metagenomeFeatures_2.4.0.zip && rm metagenomeFeatures_2.4.0.tar.gz metagenomeFeatures_2.4.0.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 2642k 100 2642k 0 0 24.1M 0 --:--:-- --:--:-- --:--:-- 25.8M install for i386 * installing *source* package 'metagenomeFeatures' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'metagenomeFeatures' finding HTML links ... done MgDb-accessor html MgDb-class html MgDb-methods html annotateFeatures-MgDb-method html get_gg13.8_85MgDb html make_mgdb_sqlite html mgFeatures-accessors html mgFeatures-class html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpeYRn7d/R.INSTALLd7449897af/metagenomeFeatures/man/mgFeatures-class.Rd:27: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic mgFeatures-methods html mock_mgF html mock_query_df html newMgDb html qiita_study_94_gg_ids html reexports html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpeYRn7d/R.INSTALLd7449897af/metagenomeFeatures/man/reexports.Rd:14: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic select-MgDb-method html taxa_ 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 'metagenomeFeatures' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'metagenomeFeatures' as metagenomeFeatures_2.4.0.zip * DONE (metagenomeFeatures) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'metagenomeFeatures' successfully unpacked and MD5 sums checked
metagenomeFeatures.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) > > test_check("metagenomeFeatures") Loading required package: metagenomeFeatures Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'dplyr' The following object is masked from 'package:Biobase': combine The following objects are masked from 'package:BiocGenerics': combine, intersect, setdiff, union The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union == testthat results =========================================================== [ OK: 79 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 4.42 0.40 4.79 |
metagenomeFeatures.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) > > test_check("metagenomeFeatures") Loading required package: metagenomeFeatures Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'dplyr' The following object is masked from 'package:Biobase': combine The following objects are masked from 'package:BiocGenerics': combine, intersect, setdiff, union The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union == testthat results =========================================================== [ OK: 79 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 6.50 0.23 6.71 |
metagenomeFeatures.Rcheck/examples_i386/metagenomeFeatures-Ex.timings
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metagenomeFeatures.Rcheck/examples_x64/metagenomeFeatures-Ex.timings
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