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Package 74/479HostnameOS / ArchBUILDCHECKBUILD BIN
CALIB 1.19.0
Hui Zhao
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CALIB
Last Changed Rev: 54802 / Revision: 56603
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: CALIB
Version: 1.19.0
Command: mkdir CALIB.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CALIB.buildbin-libdir CALIB_1.19.0.tar.gz >CALIB-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=CALIB.buildbin-libdir --install="check:CALIB-install.out" --force-multiarch --no-vignettes --timings CALIB_1.19.0.tar.gz && mv CALIB.buildbin-libdir/* CALIB.Rcheck/ && rmdir CALIB.buildbin-libdir
StartedAt: 2011-07-07 04:25:34 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 04:27:36 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 121.9 seconds
RetCode: 0
Status:  OK  
CheckDir: CALIB.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/CALIB.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CALIB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CALIB' version '1.19.0'
* 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 installed package size ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                old_size new_size compress
  RG.rda           798Kb    430Kb       xz
  normdata.rda     309Kb    262Kb       xz
  parameter.rda    158Kb     69Kb       xz
  spike.rda        166Kb     73Kb       xz
* 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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

CALIB.Rcheck/00install.out:


install for i386

* installing *source* package 'CALIB' ...
** libs
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c Design.cpp -o Design.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c Estimation.cpp -o Estimation.o
Estimation.cpp: In function 'SEXPREC* estimation(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c NormalizedData.cpp -o NormalizedData.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c ParameterofOneArray.cpp -o ParameterofOneArray.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c RawDataofOneArray.cpp -o RawDataofOneArray.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c SpikeofOneArray.cpp -o SpikeofOneArray.o
g++ -shared -s -static-libgcc -o CALIB.dll tmp.def Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/CALIB.buildbin-libdir/CALIB/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'quickstart.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'CALIB' ...
** libs
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c Design.cpp -o Design.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c Estimation.cpp -o Estimation.o
Estimation.cpp: In function 'SEXPREC* estimation(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
Estimation.cpp:144:78: warning: deprecated conversion from string constant to 'char*'
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c NormalizedData.cpp -o NormalizedData.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c ParameterofOneArray.cpp -o ParameterofOneArray.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c RawDataofOneArray.cpp -o RawDataofOneArray.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c SpikeofOneArray.cpp -o SpikeofOneArray.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o CALIB.dll tmp.def Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/CALIB.buildbin-libdir/CALIB/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CALIB' as CALIB_1.19.0.zip

* DONE (CALIB)

CALIB.Rcheck/CALIB-Ex.timings:

nameusersystemelapsed
RG0.220.000.22
adjustP20.450.000.45
calibReadMe000
cbind0.010.000.02
dim000
dimnames0.020.000.02
estimateParameter6.130.006.13
getColClasses000
merge0.020.000.01
normalizeData0.870.000.88
normdata0.120.000.12
parameter0.050.000.05
plotNormalizedData0.160.000.15
plotSpikeCI0.140.000.14
plotSpikeHI0.110.000.11
plotSpikeRG0.510.000.52
plotSpikeSpotError0.060.000.06
read.rg000
spike0.090.000.09
subsetting000