Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:38:08 -0400 (Wed, 17 Oct 2018).
Package 589/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GenomeInfoDb 1.16.0 Bioconductor Package Maintainer
| 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: GenomeInfoDb |
Version: 1.16.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomeInfoDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GenomeInfoDb_1.16.0.tar.gz |
StartedAt: 2018-10-17 02:14:53 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 02:18:38 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 224.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GenomeInfoDb.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomeInfoDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GenomeInfoDb_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GenomeInfoDb.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 'GenomeInfoDb/DESCRIPTION' ... OK * this is package 'GenomeInfoDb' version '1.16.0' * 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-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/GenomeDescription-class.Rd:45: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/GenomeDescription-class.Rd:46: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/GenomeDescription-class.Rd:126: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd:130: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:82: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:105: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:106: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:107: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:116: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:118: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:131: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:136: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:137: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:182: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:182: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:184: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:186: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:187: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:188: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:190: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:192: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:226: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:226: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:229: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:232: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:233: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:234: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:237: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:240: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.7-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 ... 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed seqlevels-wrappers 21.90 0.14 22.05 seqinfo 18.64 0.98 19.63 loadTaxonomyDb 6.34 0.75 7.12 GenomeDescription-class 5.14 0.47 5.61 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed seqinfo 23.00 0.33 23.33 seqlevels-wrappers 22.30 0.19 22.48 GenomeDescription-class 7.47 0.32 7.78 loadTaxonomyDb 6.93 0.13 7.07 fetchExtendedChromInfoFromUCSC 2.39 1.01 5.46 * 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, 1 NOTE See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GenomeInfoDb.Rcheck/00check.log' for details.
GenomeInfoDb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/GenomeInfoDb_1.16.0.tar.gz && rm -rf GenomeInfoDb.buildbin-libdir && mkdir GenomeInfoDb.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GenomeInfoDb_1.16.0.zip && rm GenomeInfoDb_1.16.0.tar.gz GenomeInfoDb_1.16.0.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 3030k 100 3030k 0 0 36.6M 0 --:--:-- --:--:-- --:--:-- 40.5M install for i386 * installing *source* package 'GenomeInfoDb' ... ** R ** inst ** byte-compile and prepare 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-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/GenomeDescription-class.Rd:45: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/GenomeDescription-class.Rd:46: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/GenomeDescription-class.Rd:126: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Seqinfo-class html fetchExtendedChromInfoFromUCSC html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd:130: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic loadTaxonomyDb html mapGenomeBuilds html rankSeqlevels html seqinfo html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:82: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:105: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:106: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:107: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:116: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:118: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:131: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:136: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:137: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:182: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:182: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:184: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:186: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:187: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:188: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:190: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:192: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:226: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:226: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:229: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:232: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:233: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:234: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:237: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/seqinfo.Rd:240: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic 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_1.16.0.zip * DONE (GenomeInfoDb) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'GenomeInfoDb' successfully unpacked and MD5 sums checked In R CMD INSTALL
GenomeInfoDb.Rcheck/tests_i386/run_unitTests.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. > 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, 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: 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 [1] TRUE > GenomeInfoDb:::.test() RUNIT TEST PROTOCOL -- Wed Oct 17 02:18:25 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 6.23 0.40 6.67 |
GenomeInfoDb.Rcheck/tests_x64/run_unitTests.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. > 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, 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: 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 [1] TRUE > GenomeInfoDb:::.test() RUNIT TEST PROTOCOL -- Wed Oct 17 02:18:32 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 6.12 0.29 6.42 |
GenomeInfoDb.Rcheck/examples_i386/GenomeInfoDb-Ex.timings
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GenomeInfoDb.Rcheck/examples_x64/GenomeInfoDb-Ex.timings
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