genoset 1.6.0
Peter M. Haverty
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/genoset | | Last Changed Rev: 64678 / Revision: 69725 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/genoset.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.6.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
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 01:12:29 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 was 1 note.
See
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/genoset.Rcheck/00check.log’
for details.
* installing *source* package ‘genoset’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c genoset.c -o genoset.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o genoset.so genoset.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/genoset.Rcheck/genoset/libs
** 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’
* DONE (genoset)