BioC 2.13: CHECK report for CALIB on perceval

Package: CALIB

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CALIB_1.28.0.tar.gz

StartedAt: 2014-04-04 23:57:57 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:59:08 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 71.0 seconds

RetCode: 0

Status:  OK

CheckDir: CALIB.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/CALIB.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.28.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CALIB’ can be installed ... [11s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘limma’ ‘methods’
A package should be listed in only one of these fields.
* 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘quickstart.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [9s/9s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/CALIB.Rcheck/00check.log’
for details.

* installing *source* package ‘CALIB’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Design.cpp -o Design.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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*’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c NormalizedData.cpp -o NormalizedData.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ParameterofOneArray.cpp -o ParameterofOneArray.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c RawDataofOneArray.cpp -o RawDataofOneArray.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c SpikeofOneArray.cpp -o SpikeofOneArray.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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-2.13-bioc/meat/CALIB.Rcheck/CALIB/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CALIB)

name	user	system	elapsed
RG	0.250	0.023	0.274
adjustP2	0.470	0.031	0.502
calibReadMe	0.015	0.002	0.016
cbind	0.037	0.001	0.038
dim	0.044	0.001	0.045
dimnames	0.093	0.008	0.100
estimateParameter	3.030	0.031	3.063
getColClasses	0.045	0.001	0.046
merge	0.058	0.002	0.060
normalizeData	0.582	0.047	0.633
normdata	0.122	0.019	0.140
parameter	0.062	0.007	0.068
plotNormalizedData	0.154	0.022	0.179
plotSpikeCI	0.183	0.049	0.237
plotSpikeHI	0.193	0.019	0.212
plotSpikeRG	0.433	0.056	0.490
plotSpikeSpotError	0.152	0.028	0.184
read.rg	0.018	0.001	0.019
spike	0.081	0.009	0.090
subsetting	0.037	0.003	0.041