Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:23:46 -0400 (Thu, 12 Apr 2018).
Package 559/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GenomeInfoDb 1.14.0 Bioconductor Package Maintainer
| 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: GenomeInfoDb |
Version: 1.14.0 |
Command: rm -rf GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && mkdir GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.14.0.tar.gz >GenomeInfoDb.Rcheck\00install.out 2>&1 && cp GenomeInfoDb.Rcheck\00install.out GenomeInfoDb-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomeInfoDb.buildbin-libdir --install="check:GenomeInfoDb-install.out" --force-multiarch --no-vignettes --timings GenomeInfoDb_1.14.0.tar.gz |
StartedAt: 2018-04-12 00:16:53 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 00:20:44 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 231.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GenomeInfoDb.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && mkdir GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.14.0.tar.gz >GenomeInfoDb.Rcheck\00install.out 2>&1 && cp GenomeInfoDb.Rcheck\00install.out GenomeInfoDb-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomeInfoDb.buildbin-libdir --install="check:GenomeInfoDb-install.out" --force-multiarch --no-vignettes --timings GenomeInfoDb_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomeInfoDb.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 'GenomeInfoDb/DESCRIPTION' ... OK * this is package 'GenomeInfoDb' version '1.14.0' * 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 'GenomeInfoDb' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/GenomeDescription-class.Rd:45: missing file link 'BSgenome' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/GenomeDescription-class.Rd:46: missing file link 'BSgenome' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/GenomeDescription-class.Rd:126: missing file link 'BSgenome' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd:130: missing file link 'getBSgenome' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:82: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:105: missing file link 'GRangesList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:106: missing file link 'GAlignmentPairs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:107: missing file link 'GAlignmentsList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:116: missing file link 'GRangesList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:118: missing file link 'exonsBy' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:131: missing file link 'GRangesList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:136: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:137: missing file link 'GAlignments' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:182: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:182: missing file link 'GRangesList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:184: missing file link 'SummarizedExperiment' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:186: missing file link 'GAlignments' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:187: missing file link 'GAlignmentPairs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:188: missing file link 'GAlignmentsList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:190: missing file link 'TxDb' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:192: missing file link 'BSgenome' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:227: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:227: missing file link 'GRangesList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:230: missing file link 'SummarizedExperiment' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:233: missing file link 'GAlignments' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:234: missing file link 'GAlignmentPairs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:235: missing file link 'GAlignmentsList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:238: missing file link 'TxDb' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:241: missing file link 'BSgenome' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomeInfoDb.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 Unexported object imported by a ':::' call: 'utils:::.roman2numeric' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .getTaxonomyId: no visible binding for global variable 'speciesMap' .lookupSpeciesFromTaxId: no visible binding for global variable 'specData' available.species: no visible binding for global variable 'speciesMap' Undefined global functions or variables: specData speciesMap * 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed seqinfo 14.74 0.14 22.31 seqlevels-wrappers 13.91 0.11 14.02 available.species 10.64 0.46 11.09 GenomeDescription-class 5.06 0.27 5.33 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed seqlevels-wrappers 18.60 0.14 18.73 seqinfo 17.55 0.03 17.59 available.species 8.83 0.08 8.91 GenomeDescription-class 5.86 0.15 6.01 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'run_unitTests.R' OK ** running tests for arch 'x64' ... Running 'run_unitTests.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, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomeInfoDb.Rcheck/00check.log' for details.
GenomeInfoDb.Rcheck/00install.out
install for i386 * installing *source* package 'GenomeInfoDb' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'GenomeInfoDb' finding HTML links ... done GenomeDescription-class html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/GenomeDescription-class.Rd:45: missing file link 'BSgenome' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/GenomeDescription-class.Rd:46: missing file link 'BSgenome' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/GenomeDescription-class.Rd:126: missing file link 'BSgenome' Seqinfo-class html available.species html fetchExtendedChromInfoFromUCSC html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd:130: missing file link 'getBSgenome' mapGenomeBuilds html rankSeqlevels html seqinfo html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:82: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:105: missing file link 'GRangesList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:106: missing file link 'GAlignmentPairs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:107: missing file link 'GAlignmentsList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:116: missing file link 'GRangesList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:118: missing file link 'exonsBy' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:131: missing file link 'GRangesList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:136: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:137: missing file link 'GAlignments' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:182: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:182: missing file link 'GRangesList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:184: missing file link 'SummarizedExperiment' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:186: missing file link 'GAlignments' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:187: missing file link 'GAlignmentPairs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:188: missing file link 'GAlignmentsList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:190: missing file link 'TxDb' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:192: missing file link 'BSgenome' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:227: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:227: missing file link 'GRangesList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:230: missing file link 'SummarizedExperiment' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:233: missing file link 'GAlignments' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:234: missing file link 'GAlignmentPairs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:235: missing file link 'GAlignmentsList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:238: missing file link 'TxDb' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:241: missing file link 'BSgenome' seqlevels-wrappers html seqlevelsStyle html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'GenomeInfoDb' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'GenomeInfoDb' as GenomeInfoDb_1.14.0.zip * DONE (GenomeInfoDb) In R CMD INSTALL In R CMD INSTALL
GenomeInfoDb.Rcheck/tests_i386/run_unitTests.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. > require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package") Loading required package: GenomeInfoDb 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 Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges [1] TRUE > GenomeInfoDb:::.test() RUNIT TEST PROTOCOL -- Thu Apr 12 00:20:22 2018 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomeInfoDb RUnit Tests - 20 test functions, 0 errors, 0 failures Number of test functions: 20 Number of errors: 0 Number of failures: 0 Warning messages: 1: In .Seqinfo.mergexy(x, y) : Each of the 2 combined objects has sequence levels not in the other: - in 'x': chr1, chr2 - in 'y': chr4 Make sure to always combine/compare objects based on the same reference genome (use suppressWarnings() to suppress this warning). 2: 'organism' not found: nothere 3: 'organism' not found: nothere 4: 'genome' not found: nothere 5: 'genome' not found: nothere > > proc.time() user system elapsed 12.06 0.37 12.45 |
GenomeInfoDb.Rcheck/tests_x64/run_unitTests.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. > require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package") Loading required package: GenomeInfoDb 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 Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges [1] TRUE > GenomeInfoDb:::.test() RUNIT TEST PROTOCOL -- Thu Apr 12 00:20:38 2018 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomeInfoDb RUnit Tests - 20 test functions, 0 errors, 0 failures Number of test functions: 20 Number of errors: 0 Number of failures: 0 Warning messages: 1: In .Seqinfo.mergexy(x, y) : Each of the 2 combined objects has sequence levels not in the other: - in 'x': chr1, chr2 - in 'y': chr4 Make sure to always combine/compare objects based on the same reference genome (use suppressWarnings() to suppress this warning). 2: 'organism' not found: nothere 3: 'organism' not found: nothere 4: 'genome' not found: nothere 5: 'genome' not found: nothere > > proc.time() user system elapsed 14.57 0.35 14.96 |
GenomeInfoDb.Rcheck/examples_i386/GenomeInfoDb-Ex.timings
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GenomeInfoDb.Rcheck/examples_x64/GenomeInfoDb-Ex.timings
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