Package: CALIB

Version: 1.2.0

Command: D:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD check CALIB_1.2.0.tar.gz

RetCode: 0

Time: 216.3 seconds

Status: OK

CheckDir: CALIB.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.0-bioc/meat/CALIB.Rcheck'
* using R version 2.5.1 (2007-06-27)
* checking for file 'CALIB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CALIB' version '1.2.0'
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... 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

installing R.css in D:/biocbld/bbs-2.0-bioc/meat/CALIB.Rcheck


---------- Making package CALIB ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making Design.d from Design.cpp
making Estimation.d from Estimation.cpp
making NormalizedData.d from NormalizedData.cpp
making ParameterofOneArray.d from ParameterofOneArray.cpp
making RawDataofOneArray.d from RawDataofOneArray.cpp
making SpikeofOneArray.d from SpikeofOneArray.cpp
g++   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O2   -c Design.cpp -o Design.o
g++   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O2   -c Estimation.cpp -o Estimation.o
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In copy constructor `std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = std::string, _Alloc = std::allocator<std::string>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In copy constructor `Spike::Spike(const Spike&)':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h: In member function `std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = std::string, _Alloc = std::allocator<std::string>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h:715: warning: '__result' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h: In member function `std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ParameterofOneArray, _Alloc = std::allocator<ParameterofOneArray>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h:715: warning: '__result' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h: In member function `std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Design, _Alloc = std::allocator<Design>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h:715: warning: '__result' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h: In member function `std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = RawDataofOneArray, _Alloc = std::allocator<RawDataofOneArray>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h:715: warning: '__result' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h: In member function `std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = NDataofOneGene, _Alloc = std::allocator<NDataofOneGene>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h:715: warning: '__result' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In function `SEXPREC* estimation(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In function `SEXPREC* normalization(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
g++   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O2   -c NormalizedData.cpp -o NormalizedData.o
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In copy constructor `std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = std::string, _Alloc = std::allocator<std::string>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In member function `std::vector<std::string, std::allocator<std::string> > NormalizedData::getCloneID()':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In member function `std::vector<NDataofOneGene, std::allocator<NDataofOneGene> > NormalizedData::getData()':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In copy constructor `std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = ParameterofOneArray, _Alloc = std::allocator<ParameterofOneArray>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h: In member function `std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = std::string, _Alloc = std::allocator<std::string>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h:715: warning: '__result' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h: In member function `std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = RawDataofOneArray, _Alloc = std::allocator<RawDataofOneArray>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h:715: warning: '__result' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
g++   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O2   -c ParameterofOneArray.cpp -o ParameterofOneArray.o
g++   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O2   -c RawDataofOneArray.cpp -o RawDataofOneArray.o
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In copy constructor `std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = std::string, _Alloc = std::allocator<std::string>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In member function `std::vector<std::string, std::allocator<std::string> > RawDataofOneArray::getCloneID()':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h: In member function `std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = std::string, _Alloc = std::allocator<std::string>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h:715: warning: '__result' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
g++   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O2   -c SpikeofOneArray.cpp -o SpikeofOneArray.o
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In member function `std::vector<std::string, std::allocator<std::string> > SpikeofOneArray::getType(Spike)':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In member function `std::vector<std::string, std::allocator<std::string> > SpikeofOneArray::getType()':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In member function `std::vector<std::string, std::allocator<std::string> > SpikeofOneArray::getSpotID(Spike)':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In member function `std::vector<std::string, std::allocator<std::string> > SpikeofOneArray::getSpotID()':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h: In member function `std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = std::string, _Alloc = std::allocator<std::string>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_vector.h:715: warning: '__result' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
windres -I d:/biocbld/bbs-2.0-bioc/R/include  -i CALIB_res.rc -o CALIB_res.o
g++  -shared -s  -o CALIB.dll CALIB.def Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o CALIB_res.o  -Ld:/biocbld/bbs-2.0-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'CALIB'
     Formats: text html latex example chm 
  ParameterList-class               text    html    latex           chm
  RG                                text    html    latex   example chm
  RGList_CALIB-class                text    html    latex           chm
  SpikeList-class                   text    html    latex           chm
  adjustP2                          text    html    latex   example chm
  calibReadMe                       text    html    latex   example chm
  cbind                             text    html    latex   example chm
  dim                               text    html    latex   example chm
  dimnames                          text    html    latex   example chm
  estimateParameter                 text    html    latex   example chm
  getColClasses                     text    html    latex   example chm
  merge                             text    html    latex   example chm
  normalizeData                     text    html    latex   example chm
  normdata                          text    html    latex   example chm
  parameter                         text    html    latex   example chm
  plotNormalizedData                text    html    latex   example chm
  plotSpikeCI                       text    html    latex   example chm
  plotSpikeHI                       text    html    latex   example chm
  plotSpikeRG                       text    html    latex   example chm
  plotSpikeSpotError                text    html    latex   example chm
  read.rg                           text    html    latex   example chm
  read.spike                        text    html    latex           chm
  spike                             text    html    latex   example chm
  subset                            text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.0-bioc\meat\CALIB.Rcheck\00_pkg_src\CALIB\chm\CALIB.chm


Compile time: 0 minutes, 0 seconds
25	Topics
124	Local links
0	Internet links
1	Graphic


Created d:\biocbld\bbs-2.0-bioc\meat\CALIB.Rcheck\00_pkg_src\CALIB\chm\CALIB.chm, 54,730 bytes
Compression decreased file by 66,817 bytes.
  preparing package CALIB for lazy loading
Loading required package: limma
  adding MD5 sums

* DONE (CALIB)