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Package 226/553HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: genoset
Version: 1.6.0
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings genoset_1.6.0.tar.gz
StartedAt: 2012-09-24 01:08:45 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 01:12:33 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 228.0 seconds
RetCode: 0
Status:  OK 
CheckDir: genoset.Rcheck
Warnings: 0

Command output

* 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.

genoset.Rcheck/00install.out:

* 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)

genoset.Rcheck/genoset-Ex.timings:

nameusersystemelapsed
BAFSet0.6280.0000.629
BAFSet.to.ExpressionSets0.1600.0000.157
CNSet0.1080.0000.108
GenoSet0.3840.0040.387
baf0.0280.0080.034
baf2mbaf0.0280.0000.026
bafset-class0.1400.0040.142
boundingIndices0.0000.0000.001
boundingIndices2000
chr-methods0.0880.0000.090
chrIndices-methods0.0160.0000.017
chrInfo0.0240.0040.025
chrNames0.0880.0000.090
chrOrder0.0000.0000.001
cn0.0200.0120.032
cnset-class0.0840.0000.088
colMeans0.0080.0000.008
convertToBigMatrix000
gcCorrect0.0080.0000.008
genoPlot-methods0.0600.0040.063
genoPos-methods0.0320.0160.046
genomeAxis0.0440.0000.042
genoset-class0.0880.0000.088
genoset-methods0.5560.0040.561
initGenoSet0.0880.0000.090
isGenomeOrder-methods0.0200.0000.018
locData0.0360.0080.042
lrr0.0280.0040.032
modeCenter0.0040.0000.007
pos0.0880.0000.089
rangeSampleMeans0.1080.0000.107
readGenoSet000
runCBS2.4120.0002.414
segTable-methods2.1480.0002.145
segs2Rle1.8410.0001.840
segs2RleDataFrame2.1440.0002.185
subsetAssayData0.0120.0000.015
toGenomeOrder-methods0.8480.0000.886
universe0.0160.0000.017