Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:21:29 -0400 (Thu, 12 Apr 2018).
Package 399/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
easyRNASeq 2.14.0 Nicolas Delhomme
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: easyRNASeq |
Version: 2.14.0 |
Command: rm -rf easyRNASeq.buildbin-libdir easyRNASeq.Rcheck && mkdir easyRNASeq.buildbin-libdir easyRNASeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=easyRNASeq.buildbin-libdir easyRNASeq_2.14.0.tar.gz >easyRNASeq.Rcheck\00install.out 2>&1 && cp easyRNASeq.Rcheck\00install.out easyRNASeq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=easyRNASeq.buildbin-libdir --install="check:easyRNASeq-install.out" --force-multiarch --no-vignettes --timings easyRNASeq_2.14.0.tar.gz |
StartedAt: 2018-04-11 23:40:48 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 23:47:21 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 392.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: easyRNASeq.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf easyRNASeq.buildbin-libdir easyRNASeq.Rcheck && mkdir easyRNASeq.buildbin-libdir easyRNASeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=easyRNASeq.buildbin-libdir easyRNASeq_2.14.0.tar.gz >easyRNASeq.Rcheck\00install.out 2>&1 && cp easyRNASeq.Rcheck\00install.out easyRNASeq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=easyRNASeq.buildbin-libdir --install="check:easyRNASeq-install.out" --force-multiarch --no-vignettes --timings easyRNASeq_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/easyRNASeq.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 'easyRNASeq/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'easyRNASeq' version '2.14.0' * 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 'easyRNASeq' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/GenomicRanges-methods.Rd:20: missing file link 'colnames' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/GenomicRanges-methods.Rd:22: missing file link 'colnames' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/GenomicRanges-methods.Rd:99: missing file link 'colnames' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd:14: missing file link 'summarizeOverlaps' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd:39: missing file link 'summarizeOverlaps' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-annotation-methods.Rd:38: missing file link 'readGff3' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-package.Rd:129: missing file link 'BamFileList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/genomeIntervals-methods.Rd:39: missing file link 'readGff3' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/parallel-methods.Rd:44: missing file link 'makePSOCKcluster' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/parallel-methods.Rd:45: missing file link 'stopCluster' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/easyRNASeq.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 ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: '.convertToUCSC' * 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 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: 1 WARNING, 1 NOTE See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/easyRNASeq.Rcheck/00check.log' for details.
easyRNASeq.Rcheck/00install.out
install for i386 * installing *source* package 'easyRNASeq' ... ** R ** data ** inst ** preparing package for lazy loading Creating a generic function for 'basename' from package 'base' in package 'easyRNASeq' Creating a generic function for 'file.exists' from package 'base' in package 'easyRNASeq' ** help *** installing help indices converting help for package 'easyRNASeq' finding HTML links ... done DESeq-methods html finding level-2 HTML links ... done GenomicRanges-methods html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/GenomicRanges-methods.Rd:20: missing file link 'colnames' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/GenomicRanges-methods.Rd:22: missing file link 'colnames' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/GenomicRanges-methods.Rd:99: missing file link 'colnames' IRanges-methods html Rsamtools-methods html ShortRead-methods html basename-methods html easyRNASeq-AnnotParam-accessors html easyRNASeq-AnnotParam-class html easyRNASeq-AnnotParam html easyRNASeq-BamFileList html easyRNASeq-BamParam-accessors html easyRNASeq-BamParam-class html easyRNASeq-BamParam html easyRNASeq-RnaSeqParam-accessors html easyRNASeq-RnaSeqParam-class html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd:14: missing file link 'summarizeOverlaps' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd:39: missing file link 'summarizeOverlaps' easyRNASeq-RnaSeqParam html easyRNASeq-accessors html easyRNASeq-annotation-internal-methods html easyRNASeq-annotation-methods html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-annotation-methods.Rd:38: missing file link 'readGff3' easyRNASeq-class html easyRNASeq-correction-methods html easyRNASeq-coverage-methods html easyRNASeq-datasets html easyRNASeq-defunct-annotation-methods html easyRNASeq-defunct html easyRNASeq-deprecated html easyRNASeq-easyRNASeq html easyRNASeq-global-variables html easyRNASeq-internal-AnnotParam-methods html easyRNASeq-internal-methods html easyRNASeq-island-methods html easyRNASeq-package html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-package.Rd:129: missing file link 'BamFileList' easyRNASeq-simpleRNASeq html easyRNASeq-summarization-internal-methods html easyRNASeq-summarization-methods html easyRNASeq-synthetic-transcripts html edgeR-methods html file.exists-methods html genomeIntervals-methods html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/genomeIntervals-methods.Rd:39: missing file link 'readGff3' parallel-methods html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/parallel-methods.Rd:44: missing file link 'makePSOCKcluster' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/parallel-methods.Rd:45: missing file link 'stopCluster' print-methods html show-methods html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'easyRNASeq' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'easyRNASeq' as easyRNASeq_2.14.0.zip * DONE (easyRNASeq) In R CMD INSTALL In R CMD INSTALL
easyRNASeq.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("easyRNASeq") Loading required package: GenomicRanges Loading required package: stats4 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: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb No validation performed at that stage Validated a datasource of type biomaRt No validation performed at that stage Validated a datasource of type rda Read 999 records Validated a datasource of type gff3 RUNIT TEST PROTOCOL -- Wed Apr 11 23:46:13 2018 *********************************************** Number of test functions: 21 Number of errors: 0 Number of failures: 0 1 Test Suite : easyRNASeq RUnit Tests - 21 test functions, 0 errors, 0 failures Number of test functions: 21 Number of errors: 0 Number of failures: 0 There were 13 warnings (use warnings() to see them) > > > proc.time() user system elapsed 39.62 1.39 48.35 |
easyRNASeq.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("easyRNASeq") Loading required package: GenomicRanges Loading required package: stats4 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: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb No validation performed at that stage Validated a datasource of type biomaRt No validation performed at that stage Validated a datasource of type rda Read 999 records Validated a datasource of type gff3 RUNIT TEST PROTOCOL -- Wed Apr 11 23:47:14 2018 *********************************************** Number of test functions: 21 Number of errors: 0 Number of failures: 0 1 Test Suite : easyRNASeq RUnit Tests - 21 test functions, 0 errors, 0 failures Number of test functions: 21 Number of errors: 0 Number of failures: 0 There were 13 warnings (use warnings() to see them) > > > proc.time() user system elapsed 55.01 1.25 60.64 |
easyRNASeq.Rcheck/examples_i386/easyRNASeq-Ex.timings
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easyRNASeq.Rcheck/examples_x64/easyRNASeq-Ex.timings
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