genomeIntervals 1.18.0
Julien Gagneur
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/genomeIntervals | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/genomeIntervals.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.18.0'
* 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 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'methods'
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: 'Biobase'
All declared Imports should be used.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'genomeIntervals.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [5s] OK
** running examples for arch 'x64' ... [6s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
Running 'benchmarking-tests.R' [6s]
Comparing 'benchmarking-tests.Rout' to 'benchmarking-tests.Rout.save' ...13,37d12
<
< 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, append,
< as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq,
< get, intersect, is.unsorted, 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 by 'intervals::coerce' when loading 'genomeIntervals'
< 2: replacing previous import by 'intervals::initialize' when loading 'genomeIntervals'
Running 'consistency-tests.R' [4s]
Running 'fullShow.R' [0s]
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-2.13-bioc\tmpdir\RtmpUXhlmV\Rdiffa1ab01122513e" "D:\biocbld\bbs-2.13-bioc\tmpdir\RtmpUXhlmV\Rdiffb1ab072e973e9"' had status 1
[14s] OK
** running tests for arch 'x64'
Running 'benchmarking-tests.R' [4s]
Comparing 'benchmarking-tests.Rout' to 'benchmarking-tests.Rout.save' ...13,37d12
<
< 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, append,
< as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq,
< get, intersect, is.unsorted, 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 by 'intervals::coerce' when loading 'genomeIntervals'
< 2: replacing previous import by 'intervals::initialize' when loading 'genomeIntervals'
Running 'consistency-tests.R' [6s]
Running 'fullShow.R' [0s]
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-2.13-bioc\tmpdir\Rtmpe4r2IK\Rdiffa2b88e572401" "D:\biocbld\bbs-2.13-bioc\tmpdir\Rtmpe4r2IK\Rdiffb2b886f9420d3"' had status 1
[12s] 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
NOTE: There were 3 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/genomeIntervals.Rcheck/00check.log'
for details.