* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/genoset.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 '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 whether package 'genoset' can be installed ... 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
* 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: '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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-2.13-bioc/meat/genoset.buildbin-libdir/genoset/libs/i386/genoset.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/genoset.buildbin-libdir/genoset/libs/x64/genoset.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [20s] OK
** running examples for arch 'x64' ... [19s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
Running 'prove.R' [34s]
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
< 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
---
> 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'
33a35,36
> Loading required namespace: DNAcopy
> Using mclapply for segmentation ...
35a39
> Using mclapply for segmentation ...
37a42
> Using mclapply for segmentation ...
39a45
> Using mclapply for segmentation ...
41a48
> Using mclapply for segmentation ...
43a51
> Using mclapply for segmentation ...
45a54
> Using mclapply for segmentation ...
47a57
> Using mclapply for segmentation ...
49a60
> Using mclapply for segmentation ...
51a63
> Using mclapply for segmentation ...
56c68
< RUNIT TEST PROTOCOL -- Sat Apr 05 04:14:09 2014
---
> RUNIT TEST PROTOCOL -- Thu Oct 25 19:26:26 2012
58c70
< Number of test functions: 26
---
> Number of test functions: 24
64,65c76,77
< 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
68c80
< There were 35 warnings (use warnings() to see them)
---
> There were 37 warnings (use warnings() to see them)
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-2.13-bioc\tmpdir\RtmpuiPamp\Rdiffa2b8823301a09" "D:\biocbld\bbs-2.13-bioc\tmpdir\RtmpuiPamp\Rdiffb2b8868bd164a"' had status 1
[35s] OK
** running tests for arch 'x64'
Running 'prove.R' [32s]
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
< 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
---
> 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'
33a35,36
> Loading required namespace: DNAcopy
> Using mclapply for segmentation ...
35a39
> Using mclapply for segmentation ...
37a42
> Using mclapply for segmentation ...
39a45
> Using mclapply for segmentation ...
41a48
> Using mclapply for segmentation ...
43a51
> Using mclapply for segmentation ...
45a54
> Using mclapply for segmentation ...
47a57
> Using mclapply for segmentation ...
49a60
> Using mclapply for segmentation ...
51a63
> Using mclapply for segmentation ...
56c68
< RUNIT TEST PROTOCOL -- Sat Apr 05 04:14:42 2014
---
> RUNIT TEST PROTOCOL -- Thu Oct 25 19:26:26 2012
58c70
< Number of test functions: 26
---
> Number of test functions: 24
64,65c76,77
< 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
68c80
< There were 35 warnings (use warnings() to see them)
---
> There were 37 warnings (use warnings() to see them)
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-2.13-bioc\tmpdir\RtmpMvvxR8\Rdiffa18886dc0342f" "D:\biocbld\bbs-2.13-bioc\tmpdir\RtmpMvvxR8\Rdiffb188837806685"' had status 1
[33s] 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/genoset.Rcheck/00check.log'
for details.