genoset 1.16.2
Peter M. Haverty
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/genoset | | Last Changed Rev: 89646 / Revision: 95116 | | Last Changed Date: 2014-04-29 11:27:54 -0700 (Tue, 29 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genoset_1.16.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/genoset.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.16.2’
* 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 ... [35s/35s] OK
* 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
* 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 ... [21s/22s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘prove.R’ [29s/27s]
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':
19,24c13,16
< anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
< do.call, 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
31a24,30
>
> Attaching package: 'Biobase'
>
> The following object(s) are masked from 'package:BiocGenerics':
>
> annotation, annotation<-
>
32a32,33
> Warning message:
> replacing previous import 'annotation' when loading 'Biobase'
33a35,38
> Loading required namespace: DNAcopy
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
> Working on segmentation for sample number 2 : a2
37a43
> Working on segmentation for sample number 1 : a1
39c45,46
<
---
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
41c48,60
<
---
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
> Working on segmentation for sample number 2 : a2
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
> Working on segmentation for sample number 2 : a2
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
> Working on segmentation for sample number 2 : a2
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
> Working on segmentation for sample number 2 : a2
> Using mclapply for segmentation ...
49c68
< RUNIT TEST PROTOCOL -- Tue Oct 7 22:17:17 2014
---
> RUNIT TEST PROTOCOL -- Thu Oct 25 19:26:26 2012
51c70
< Number of test functions: 27
---
> Number of test functions: 24
57,58c76,77
< genoset RUnit Tests - 27 test functions, 0 errors, 0 failures
< Number of test functions: 27
---
> genoset RUnit Tests - 24 test functions, 0 errors, 0 failures
> Number of test functions: 24
60a80
> There were 37 warnings (use warnings() to see them)
Warning messages:
1: In readLines(from) : line 61 appears to contain an embedded nul
2: In readLines(from) : line 63 appears to contain an embedded nul
[30s/28s] 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 was 1 note.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/genoset.Rcheck/00check.log’
for details.