BioC 2.8: CHECK report for cn.farms on liverpool

Package: cn.farms

Version: 1.0.12

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch cn.farms_1.0.12.tar.gz

StartedAt: 2011-10-20 14:42:39 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:45:00 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 140.4 seconds

RetCode: 0

Status: OK

CheckDir: cn.farms.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/cn.farms.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cn.farms/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.farms' version '1.0.12'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'cn.farms' 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
* 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 ... OK
* 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 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 examples ... 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

* installing *source* package 'cn.farms' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
laplace.cpp:420:6: warning: unused variable 'method'
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:197:9: warning: 'I1left' may be used uninitialized in this function
laplace.cpp:198:9: warning: 'I1right' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c sparse_farms.c -o sparse_farms.o
sparse_farms.c: In function 'normData':
sparse_farms.c:191:10: warning: unused variable 'k'
sparse_farms.c:191:6: warning: unused variable 'i'
sparse_farms.c: In function 'sparseFarmsC':
sparse_farms.c:262:41: warning: unused variable 'invpPsi'
sparse_farms.c:259:9: warning: unused variable 'sumhelp'
g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/cn.farms.Rcheck/cn.farms/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
================================================================================
Welcome to oligoClasses version 1.14.0
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: E:/biocbld/BBS-2˜1.8-B/meat/CNFARM˜1.RCH/00_PKG˜1/CN3367˜1.FAR
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Use options(cluster=makeCluster(...))
================================================================================

**************************************************************************
   The plan to change the data format for CNA object has been postponed   
 in order to ensure backward compatibility with older versions of DNAcopy 
**************************************************************************

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.14.0
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: E:/biocbld/BBS-2˜1.8-B/meat/CNFARM˜1.RCH/00_PKG˜1/CN3367˜1.FAR
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Use options(cluster=makeCluster(...))
================================================================================

* DONE (cn.farms)

name	user	system	elapsed
combineData	1.00	0.00	1.06
createAnnotation	0	0	0
distributionDistance	0.48	0.00	0.48
dnaCopySf	0.17	0.02	0.19
fragLengCorr	4.55	0.00	4.54
mlSummarization	2.06	0.05	2.11
normalizeAverage	0	0	0
normalizeCels	0	0	0
normalizeNpData	0	0	0
plotDendrogram	0.47	0.00	0.47
plotDensity	1.14	0.00	1.14
plotEvalIc	0.25	0.02	0.33
plotRegions	0.28	0.00	0.28
plotSmoothScatter	1.19	0.00	1.20
plotViolines	0.20	0.01	0.22
slSummarization	1.79	0.00	1.80
sparseFarmsC	0.01	0.00	0.01
summarizeFarmsExact	0	0	0
summarizeFarmsGaussian	0	0	0
summarizeFarmsMethods	0	0	0
summarizeFarmsVariational	0.02	0.00	0.02
summarizeWindowBps	0	0	0
summarizeWindowMethods	0	0	0
summarizeWindowStd	0.01	0.00	0.01

Summary

Command output