genoset 1.14.0
Peter M. Haverty
| 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/genoset | | 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 ‘/Users/biocbuild/bbs-2.13-bioc/meat/genoset.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘genoset’ can be installed ... [30s/30s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘IRanges’ ‘GenomicRanges’
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
* 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: ‘BiocGenerics:::testPackage’
See the note in ?`:::` about the use of this operator.
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘prove.R’ [39s/36s]
Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...7,13c7
< 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':
---
> The following object(s) are masked from 'package:stats':
17c11
< The following objects are masked from 'package:base':
---
> The following object(s) are masked from 'package:base':
19,23c13,16
< anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
< duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted,
< lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
< pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames,
< sapply, setdiff, sort, table, tapply, union, unique, unlist
---
> Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
> colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
> order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
> rownames, sapply, setdiff, table, tapply, union, unique
30a24,30
>
> Attaching package: 'Biobase'
>
> The following object(s) are masked from 'package:BiocGenerics':
>
> annotation, annotation<-
>
31a32,33
> Warning message:
> replacing previous import 'annotation' when loading 'Biobase'
32a35
> Loading required namespace: DNAcopy
37d39
< Working on segmentation for sample number 2 : a2
38a41
> Working on segmentation for sample number 2 : a2
43d45
< Working on segmentation for sample number 2 : a2
44a47
> Working on segmentation for sample number 2 : a2
58d60
< Working on segmentation for sample number 2 : a2
60d61
< Using mclapply for segmentation ...
61a63
> Using mclapply for segmentation ...
62a65
> Working on segmentation for sample number 2 : a2
65c68
< RUNIT TEST PROTOCOL -- Sat Apr 5 01:39:23 2014
---
> RUNIT TEST PROTOCOL -- Thu Oct 25 19:26:26 2012
67c70
< Number of test functions: 26
---
> Number of test functions: 24
73,74c76,77
< genoset RUnit Tests - 26 test functions, 0 errors, 0 failures
< Number of test functions: 26
---
> genoset RUnit Tests - 24 test functions, 0 errors, 0 failures
> Number of test functions: 24
77c80
< There were 35 warnings (use warnings() to see them)
---
> There were 37 warnings (use warnings() to see them)
[40s/36s] 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 2 notes.
See
‘/Users/biocbuild/bbs-2.13-bioc/meat/genoset.Rcheck/00check.log’
for details.