Package: CALIB

Version: 1.17.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings CALIB_1.17.0.tar.gz

StartedAt: 2011-02-24 18:31:15 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:32:26 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 70.8 seconds

RetCode: 0

Status:  OK

CheckDir: CALIB.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/CALIB.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CALIB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CALIB’ version ‘1.17.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘CALIB’ can be installed ... 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
getColClasses: no visible global function definition for ‘namesInFun’
plotSpikeCI: no visible binding for global variable ‘otherindex’
read.rg: no visible global function definition for ‘readBlueFuseHeader’
read.spike: no visible binding for global variable ‘files’
* 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘CALIB’ ...
** libs
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Design.cpp -o Design.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Estimation.cpp -o Estimation.o
Estimation.cpp: In function ‘SEXPREC* estimation(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
Estimation.cpp:144: warning: deprecated conversion from string constant to ‘char*’
Estimation.cpp:144: warning: deprecated conversion from string constant to ‘char*’
Estimation.cpp:144: warning: deprecated conversion from string constant to ‘char*’
Estimation.cpp:144: warning: deprecated conversion from string constant to ‘char*’
Estimation.cpp:144: warning: deprecated conversion from string constant to ‘char*’
Estimation.cpp:144: warning: deprecated conversion from string constant to ‘char*’
Estimation.cpp:144: warning: deprecated conversion from string constant to ‘char*’
Estimation.cpp:144: warning: deprecated conversion from string constant to ‘char*’
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c NormalizedData.cpp -o NormalizedData.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c ParameterofOneArray.cpp -o ParameterofOneArray.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c RawDataofOneArray.cpp -o RawDataofOneArray.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c SpikeofOneArray.cpp -o SpikeofOneArray.o
g++ -shared -L/usr/local/lib64 -o CALIB.so Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/CALIB.Rcheck/CALIB/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (CALIB)

name	user	system	elapsed
RG	0.104	0.016	0.170
adjustP2	0.344	0.008	0.364
calibReadMe	0.004	0.000	0.003
cbind	0.004	0.000	0.004
dim	0.004	0.000	0.004
dimnames	0.004	0.000	0.003
estimateParameter	6.360	0.028	6.471
getColClasses	0	0	0
merge	0.004	0.004	0.007
normalizeData	0.608	0.020	0.634
normdata	0.068	0.000	0.068
parameter	0.028	0.000	0.027
plotNormalizedData	0.068	0.000	0.068
plotSpikeCI	0.088	0.000	0.091
plotSpikeHI	0.060	0.000	0.063
plotSpikeRG	0.348	0.004	0.353
plotSpikeSpotError	0.096	0.000	0.094
read.rg	0.000	0.000	0.001
spike	0.028	0.000	0.029
subsetting	0.004	0.000	0.003