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Package 76/514HostnameOS / ArchBUILDCHECKBUILD BIN
CALIB 1.20.0
Hui Zhao
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/CALIB
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: CALIB
Version: 1.20.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings CALIB_1.20.0.tar.gz
StartedAt: 2012-03-23 23:34:02 -0700 (Fri, 23 Mar 2012)
EndedAt: 2012-03-23 23:35:11 -0700 (Fri, 23 Mar 2012)
EllapsedTime: 69.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CALIB.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/CALIB.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.20.0’
* 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 ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    arraydata   2.2Mb
    data        1.4Mb
    libs        4.2Mb
* 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 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
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 R CMD build --resave-data
                old_size new_size compress
  RG.rda           798Kb    436Kb       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 compiled code ... 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

CALIB.Rcheck/00install.out:

* installing *source* package ‘CALIB’ ...
** libs
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Design.cpp -o Design.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -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/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c NormalizedData.cpp -o NormalizedData.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c ParameterofOneArray.cpp -o ParameterofOneArray.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c RawDataofOneArray.cpp -o RawDataofOneArray.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c SpikeofOneArray.cpp -o SpikeofOneArray.o
g++ -shared -L/usr/local/lib64 -o CALIB.so Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/CALIB.Rcheck/CALIB/libs
** 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

* DONE (CALIB)

CALIB.Rcheck/CALIB-Ex.timings:

nameusersystemelapsed
RG0.1920.0120.204
adjustP20.4040.0040.413
calibReadMe0.0000.0040.003
cbind0.0040.0000.004
dim0.0040.0000.004
dimnames0.0000.0000.002
estimateParameter6.3440.0006.351
getColClasses0.0040.0000.000
merge0.0040.0000.006
normalizeData0.6840.0040.688
normdata0.0800.0000.086
parameter0.040.000.04
plotNormalizedData0.0880.0040.093
plotSpikeCI0.1160.0040.120
plotSpikeHI0.0720.0000.072
plotSpikeRG0.3840.0000.382
plotSpikeSpotError0.1520.0040.157
read.rg000
spike0.0320.0000.031
subsetting0.0000.0000.003