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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1
Package 44/247HostnameOSArchBUILDCHECKBUILD BIN

CALIB

1.3.1

Hui Zhao
Last Changed Date: 2007-06-10 10:22:32 -0700
Last Changed Rev: 25301
lamb1 Linux (SUSE 10.1) x86_64  OK  WARNINGS 
wellington Linux (SUSE 9.2) i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) x64  OK  WARNINGS  OK 
pitt Mac OS X (10.4.10) i386  OK [ WARNINGS ] OK 
Package: CALIB
Version: 1.3.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check CALIB_1.3.1.tar.gz
RetCode: 0
Time: 88.1 seconds
Status: WARNINGS
CheckDir: CALIB.Rcheck
Warnings: 2

Command output

* checking for working latex ... OK
* using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/CALIB.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-10 r42465)
* checking for file 'CALIB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CALIB' version '1.3.1'
* 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 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions/methods with usage in documentation object 'subset' but not in code:
  [

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'subset':
  [

Functions with \usage entries need to have the appropriate \alias entries,
and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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
* creating CALIB-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating CALIB-manual.tex ... OK
* checking CALIB-manual.tex ... OK

WARNING: There were 2 warnings, see
  /Users/biocbuild/bbs-2.1-bioc/meat/CALIB.Rcheck/00check.log
for details

CALIB.Rcheck/00install.out:

* Installing *source* package 'CALIB' ...
** libs
** arch - i386
g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c Design.cpp -o Design.o
g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c Estimation.cpp -o Estimation.o
g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c NormalizedData.cpp -o NormalizedData.o
g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c ParameterofOneArray.cpp -o ParameterofOneArray.o
g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c RawDataofOneArray.cpp -o RawDataofOneArray.o
g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c SpikeofOneArray.cpp -o SpikeofOneArray.o
g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -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
** arch - ppc
g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c Design.cpp -o Design.o
g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c Estimation.cpp -o Estimation.o
g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c NormalizedData.cpp -o NormalizedData.o
g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c ParameterofOneArray.cpp -o ParameterofOneArray.o
g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c RawDataofOneArray.cpp -o RawDataofOneArray.o
g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c SpikeofOneArray.cpp -o SpikeofOneArray.o
g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -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
** R
** data
** inst
** preparing package for lazy loading
Loading required package: limma
** help
 >>> Building/Updating help pages for package 'CALIB'
     Formats: text html latex example 
  ParameterList-class               text    html    latex
  RG                                text    html    latex   example
  RGList_CALIB-class                text    html    latex
  SpikeList-class                   text    html    latex
  adjustP2                          text    html    latex   example
  calibReadMe                       text    html    latex   example
  cbind                             text    html    latex   example
  dim                               text    html    latex   example
  dimnames                          text    html    latex   example
  estimateParameter                 text    html    latex   example
  getColClasses                     text    html    latex   example
  merge                             text    html    latex   example
  normalizeData                     text    html    latex   example
  normdata                          text    html    latex   example
  parameter                         text    html    latex   example
  plotNormalizedData                text    html    latex   example
  plotSpikeCI                       text    html    latex   example
  plotSpikeHI                       text    html    latex   example
  plotSpikeRG                       text    html    latex   example
  plotSpikeSpotError                text    html    latex   example
  read.rg                           text    html    latex   example
  read.spike                        text    html    latex
  spike                             text    html    latex   example
  subset                            text    html    latex   example
** building package indices ...
* DONE (CALIB)