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Package 450/462HostnameOS / ArchBUILDCHECKBUILD BIN
VanillaICE 1.15.0
Robert Scharpf
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE
Last Changed Rev: 54810 / Revision: 55359
Last Changed Date: 2011-04-13 18:14:51 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: VanillaICE
Version: 1.15.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings VanillaICE_1.15.0.tar.gz
StartedAt: 2011-05-09 14:32:43 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:34:26 -0700 (Mon, 09 May 2011)
EllapsedTime: 103.2 seconds
RetCode: 0
Status:  OK 
CheckDir: VanillaICE.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/VanillaICE.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VanillaICE/DESCRIPTION’ ... OK
* this is package ‘VanillaICE’ version ‘1.15.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘VanillaICE’ 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
getEmission.nps: no visible global function definition for ‘CA’
getEmission.nps: no visible global function definition for ‘getParam’
getEmission.snps: no visible global function definition for ‘CA’
getEmission.snps: no visible global function definition for ‘CB’
getEmission.snps: no visible global function definition for ‘getParam’
* checking Rd files ... NOTE
prepare_Rd: hmm.Rd:51-53: Dropping empty section \details
prepare_Rd: hmm.setup.Rd:179-181: Dropping empty section \value
prepare_Rd: hmm.setup.Rd:189-190: Dropping empty section \examples
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘DNAcopy’
* 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

VanillaICE.Rcheck/00install.out:

* installing *source* package ‘VanillaICE’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c viterbi.c -o viterbi.o
viterbi.c: In function ‘viterbi’:
viterbi.c:61:34: warning: unused variable ‘tp’
gcc -std=gnu99 -shared -L/usr/local/lib64 -o VanillaICE.so viterbi.o -lm -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/VanillaICE.Rcheck/VanillaICE/libs
** R
** data
** inst
** preparing package for lazy loading

Attaching package: ‘IRanges’

The following object(s) are masked from ‘package:base’:

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object(s) are masked from ‘package:IRanges’:

    updateObject

================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘VanillaICE.Rnw’ 
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Welcome to VanillaICE version 1.15.0

* DONE (VanillaICE)

VanillaICE.Rcheck/VanillaICE-Ex.timings:

nameusersystemelapsed
hmm3.0200.1926.250
locusLevelData0.0440.0000.046
robustSds0.0360.0040.038