Package: genoset

Version: 1.6.0

Command: rm -rf genoset.buildbin-libdir && mkdir genoset.buildbin-libdir && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genoset.buildbin-libdir genoset_1.6.0.tar.gz >genoset-install.out 2>&1 && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD check --library=genoset.buildbin-libdir --install="check:genoset-install.out" --force-multiarch --no-vignettes --timings genoset_1.6.0.tar.gz && mv genoset.buildbin-libdir/* genoset.Rcheck/ && rmdir genoset.buildbin-libdir

StartedAt: 2012-09-24 00:49:55 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:54:28 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 273.2 seconds

RetCode: 0

Status:  OK

CheckDir: genoset.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.10-bioc/meat/genoset.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-pc-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 '1.6.0'
* 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 whether package 'genoset' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... NOTE
Found the following possibly unsafe calls:
File 'R/bigmat.R':
  found unlockBinding(ad.name, aData)
* 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-2.10-bioc/meat/genoset.buildbin-libdir/genoset/libs/i386/genoset.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.10-bioc/meat/genoset.buildbin-libdir/genoset/libs/x64/genoset.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call functions 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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'prove.R'
  Comparing 'prove.Rout' to 'prove.Rout.save' ...28a29,41
> Attaching package: 'GenomicRanges'
> 
> The following object(s) are masked from 'package:BiocGenerics':
> 
>     strand, strand<-
> 
> 
> **************************************************************************
>    The plan to change the data format for CNA object has been postponed   
>  in order to ensure backward compatibility with older versions of DNAcopy 
> **************************************************************************
> 
> 
37,38c50,55
< 1: replacing previous import 'density' when loading 'stats' 
< 2: replacing previous import 'residuals' when loading 'stats' 
---
> 1: multiple methods tables found for 'strand' 
> 2: multiple methods tables found for 'strand<-' 
> 3: replacing previous import 'density' when loading 'stats' 
> 4: replacing previous import 'residuals' when loading 'stats' 
> 5: replacing previous import 'strand' when loading 'GenomicRanges' 
> 6: replacing previous import 'strand<-' when loading 'GenomicRanges' 
57c74
< RUNIT TEST PROTOCOL -- Mon Sep 24 00:53:57 2012 
---
> RUNIT TEST PROTOCOL -- Tue Mar 13 13:51:49 2012 
 OK
** running tests for arch 'x64'
  Running 'prove.R'
  Comparing 'prove.Rout' to 'prove.Rout.save' ...28a29,41
> Attaching package: 'GenomicRanges'
> 
> The following object(s) are masked from 'package:BiocGenerics':
> 
>     strand, strand<-
> 
> 
> **************************************************************************
>    The plan to change the data format for CNA object has been postponed   
>  in order to ensure backward compatibility with older versions of DNAcopy 
> **************************************************************************
> 
> 
37,38c50,55
< 1: replacing previous import 'density' when loading 'stats' 
< 2: replacing previous import 'residuals' when loading 'stats' 
---
> 1: multiple methods tables found for 'strand' 
> 2: multiple methods tables found for 'strand<-' 
> 3: replacing previous import 'density' when loading 'stats' 
> 4: replacing previous import 'residuals' when loading 'stats' 
> 5: replacing previous import 'strand' when loading 'GenomicRanges' 
> 6: replacing previous import 'strand<-' when loading 'GenomicRanges' 
57c74
< RUNIT TEST PROTOCOL -- Mon Sep 24 00:54:23 2012 
---
> RUNIT TEST PROTOCOL -- Tue Mar 13 13:51:49 2012 
 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 were 2 notes.
See
  'E:/biocbld/bbs-2.10-bioc/meat/genoset.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'genoset' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG          -O3 -Wall  -std=gnu99 -mtune=core2 -c genoset.c -o genoset.o
gcc -shared -s -static-libgcc -o genoset.dll tmp.def genoset.o -LE:/biocbld/BBS-2˜1.10-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/genoset.buildbin-libdir/genoset/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'density' when loading 'stats'
Warning: replacing previous import 'residuals' when loading 'stats'
** help
*** installing help indices
** building package indices
** installing vignettes
   'genoset.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'density' when loading 'stats'
Warning: replacing previous import 'residuals' when loading 'stats'

install for x64

* installing *source* package 'genoset' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c genoset.c -o genoset.o
gcc -m64 -shared -s -static-libgcc -o genoset.dll tmp.def genoset.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.10-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/genoset.buildbin-libdir/genoset/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'density' when loading 'stats'
Warning: replacing previous import 'residuals' when loading 'stats'
* MD5 sums
packaged installation of 'genoset' as genoset_1.6.0.zip

* DONE (genoset)