* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/genoset.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 'genoset/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genoset' version '1.12.0'
* 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 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 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 'E:/biocbld/bbs-2.12-bioc/meat/genoset.buildbin-libdir/genoset/libs/i386/genoset.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.12-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 examples ...
** running examples for arch 'i386' ... [25s] OK
** running examples for arch 'x64' ... [24s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
Running 'prove.R' [50s]
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
< 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
---
> 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'
33a36
> 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 -- Wed Oct 09 02:23:30 2013
---
> RUNIT TEST PROTOCOL -- Thu Oct 25 19:26:26 2012
68c80
< There were 50 or more warnings (use warnings() to see the first 50)
---
> There were 37 warnings (use warnings() to see them)
[51s] OK
** running tests for arch 'x64'
Running 'prove.R' [51s]
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
< 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
---
> 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'
33a36
> 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 -- Wed Oct 09 02:24:21 2013
---
> RUNIT TEST PROTOCOL -- Thu Oct 25 19:26:26 2012
68c80
< There were 50 or more warnings (use warnings() to see the first 50)
---
> There were 37 warnings (use warnings() to see them)
[52s] 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
NOTE: There was 1 note.
See
'E:/biocbld/bbs-2.12-bioc/meat/genoset.Rcheck/00check.log'
for details.