BioC 2.11: CHECK report for CALIB on perceval

Package: CALIB

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CALIB_1.24.0.tar.gz

StartedAt: 2013-03-24 22:49:30 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 22:50:41 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 70.9 seconds

RetCode: 0

Status: OK

CheckDir: CALIB.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/CALIB.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CALIB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CALIB' version '1.24.0'
* 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 'CALIB' 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 for left-over 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
read.rg: warning in scan(fullname, what = "", sep = sep, quote = quote,
  skip = 1, nlines = 1, quiet = TRUE, allowEscape = FALSE): partial
  argument match of 'allowEscape' to 'allowEscapes'
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 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 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-2.11-bioc/meat/CALIB.Rcheck/00check.log'
for details.

* installing *source* package 'CALIB' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c Design.cpp -o Design.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -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++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c NormalizedData.cpp -o NormalizedData.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c ParameterofOneArray.cpp -o ParameterofOneArray.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c RawDataofOneArray.cpp -o RawDataofOneArray.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c SpikeofOneArray.cpp -o SpikeofOneArray.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o CALIB.so Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/CALIB.Rcheck/CALIB/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'quickstart.Rnw' 
** testing if installed package can be loaded

* DONE (CALIB)

name	user	system	elapsed
RG	0.179	0.017	0.197
adjustP2	0.355	0.045	0.413
calibReadMe	0.002	0.002	0.004
cbind	0.005	0.000	0.005
dim	0.004	0.000	0.004
dimnames	0.003	0.001	0.004
estimateParameter	4.063	0.025	4.095
getColClasses	0.000	0.001	0.001
merge	0.015	0.002	0.016
normalizeData	0.564	0.026	0.680
normdata	0.105	0.014	0.120
parameter	0.056	0.004	0.059
plotNormalizedData	0.133	0.017	0.153
plotSpikeCI	0.176	0.018	0.197
plotSpikeHI	0.121	0.010	0.131
plotSpikeRG	0.405	0.043	0.454
plotSpikeSpotError	0.163	0.015	0.184
read.rg	0	0	0
spike	0.061	0.005	0.070
subsetting	0.003	0.001	0.004

Summary

Command output