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BioC 2.12: CHECK report for genomeIntervals on moscato2

This page was generated on 2013-10-09 09:38:41 -0700 (Wed, 09 Oct 2013).

Package 268/671HostnameOS / ArchBUILDCHECKBUILD BIN
genomeIntervals 1.16.0
Julien Gagneur
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/genomeIntervals
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: genomeIntervals
Version: 1.16.0
Command: rm -rf genomeIntervals.buildbin-libdir && mkdir genomeIntervals.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomeIntervals.buildbin-libdir genomeIntervals_1.16.0.tar.gz >genomeIntervals-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=genomeIntervals.buildbin-libdir --install="check:genomeIntervals-install.out" --force-multiarch --no-vignettes --timings genomeIntervals_1.16.0.tar.gz && mv genomeIntervals.buildbin-libdir/* genomeIntervals.Rcheck/ && rmdir genomeIntervals.buildbin-libdir
StartedAt: 2013-10-09 02:16:53 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:18:55 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 121.8 seconds
RetCode: 0
Status:  OK  
CheckDir: genomeIntervals.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/genomeIntervals.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genomeIntervals/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomeIntervals' version '1.16.0'
* 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 'genomeIntervals' can be installed ... OK
* checking installed package size ... OK
* checking package 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 for unstated 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [6s] OK
** running examples for arch 'x64' ... [7s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'benchmarking-tests.R' [5s]
  Comparing 'benchmarking-tests.Rout' to 'benchmarking-tests.Rout.save' ...13,36d12
< 
< 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 object is masked from 'package:stats':
< 
<     xtabs
< 
< The following objects are masked from 'package:base':
< 
<     Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
<     cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
<     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
<     rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
<     union, unique, unlist
< 
< Warning messages:
< 1: replacing previous import 'coerce' when loading 'intervals' 
< 2: replacing previous import 'initialize' when loading 'intervals' 
  Running 'consistency-tests.R' [5s]
  Running 'fullShow.R' [0s]
 [14s] OK
** running tests for arch 'x64'
  Running 'benchmarking-tests.R' [6s]
  Comparing 'benchmarking-tests.Rout' to 'benchmarking-tests.Rout.save' ...13,36d12
< 
< 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 object is masked from 'package:stats':
< 
<     xtabs
< 
< The following objects are masked from 'package:base':
< 
<     Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
<     cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
<     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
<     rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
<     union, unique, unlist
< 
< Warning messages:
< 1: replacing previous import 'coerce' when loading 'intervals' 
< 2: replacing previous import 'initialize' when loading 'intervals' 
  Running 'consistency-tests.R' [7s]
  Running 'fullShow.R' [0s]
 [14s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

genomeIntervals.Rcheck/00install.out:


install for i386

* installing *source* package 'genomeIntervals' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'coerce' when loading 'intervals'
Warning: replacing previous import 'initialize' when loading 'intervals'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'coerce' when loading 'intervals'
Warning: replacing previous import 'initialize' when loading 'intervals'

install for x64

* installing *source* package 'genomeIntervals' ...
** testing if installed package can be loaded
Warning: replacing previous import 'coerce' when loading 'intervals'
Warning: replacing previous import 'initialize' when loading 'intervals'
* MD5 sums
packaged installation of 'genomeIntervals' as genomeIntervals_1.16.0.zip
* DONE (genomeIntervals)