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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: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genoset_1.6.0.tar.gz
StartedAt: 2012-09-24 00:18:28 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:22:50 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 262.5 seconds
RetCode: 0
Status:  OK 
CheckDir: genoset.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/genoset.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 sizes of PDF files under 'inst/doc' ... 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 00:22:44 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
  '/Users/biocbuild/bbs-2.10-bioc/meat/genoset.Rcheck/00check.log'
for details.

genoset.Rcheck/00install.out:

* installing *source* package 'genoset' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c genoset.c -o genoset.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o genoset.so genoset.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.10-bioc/meat/genoset.Rcheck/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'

* DONE (genoset)

genoset.Rcheck/genoset-Ex.timings:

nameusersystemelapsed
BAFSet0.5980.0070.605
BAFSet.to.ExpressionSets0.2490.0070.258
CNSet0.3260.0010.327
GenoSet0.1360.0030.139
baf0.0510.0200.071
baf2mbaf0.0450.0030.048
bafset-class0.1990.0000.200
boundingIndices0.0010.0000.001
boundingIndices20.0010.0000.001
chr-methods0.1280.0000.128
chrIndices-methods0.0340.0020.036
chrInfo0.0460.0020.049
chrNames0.1290.0010.129
chrOrder0.0020.0000.002
cn0.0500.0200.071
cnset-class0.1270.0010.127
colMeans0.0120.0000.012
convertToBigMatrix0.0010.0000.000
gcCorrect0.0110.0010.012
genoPlot-methods0.1030.0070.111
genoPos-methods0.0660.0210.087
genomeAxis0.0680.0040.072
genoset-class0.1270.0010.127
genoset-methods0.8020.0220.823
initGenoSet0.1290.0000.129
isGenomeOrder-methods0.0340.0020.037
locData0.0630.0020.065
lrr0.0470.0180.065
modeCenter0.0100.0030.011
pos0.1270.0010.128
rangeSampleMeans0.1520.0020.154
readGenoSet000
runCBS3.5010.0143.516
segTable-methods3.0320.0153.047
segs2Rle2.7170.0132.730
segs2RleDataFrame3.0360.0153.051
subsetAssayData0.0210.0020.023
toGenomeOrder-methods0.6770.0070.685
universe0.0220.0010.023