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Package 79/462HostnameOS / ArchBUILDCHECKBUILD BIN
CGEN 1.5.0
William Wheeler
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CGEN
Last Changed Rev: 54802 / Revision: 55359
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 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: CGEN
Version: 1.5.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings CGEN_1.5.0.tar.gz
StartedAt: 2011-05-09 12:55:41 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 12:57:31 -0700 (Mon, 09 May 2011)
EllapsedTime: 110.2 seconds
RetCode: 0
Status:  OK  
CheckDir: CGEN.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/CGEN.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CGEN/DESCRIPTION' ... OK
* this is package 'CGEN' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'CGEN' 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
* 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 ... OK
* 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 ... NOTE
'library' or 'require' call not declared from: 'cluster'
* 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 examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'cluster'
* 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

CGEN.Rcheck/00install.out:

* installing *source* package 'CGEN' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c CML.c -o CML.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c ccl.c -o ccl.o
ccl.c:386:13: warning: 'tree_print' defined but not used
gfortran      -O3  -c csclust.f -o csclust.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c fsclust.c -o fsclust.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c hcl.c -o hcl.o
hcl.c:375:13: warning: 'tree_print' defined but not used
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c pmatch.c -o pmatch.o
gcc -shared -s -static-libgcc -o CGEN.dll tmp.def CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o -lgfortran -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/CGEN.Rcheck/CGEN/libs/i386
** R
** data
** exec
** inst
** preparing package for lazy loading
Loading required package: splines
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'vignette.Rnw' 
** testing if installed package can be loaded

* DONE (CGEN)

CGEN.Rcheck/CGEN-Ex.timings:

nameusersystemelapsed
LocusMapData0.030.000.03
QQ.plot0.010.000.02
SNPdata0.020.000.01
Xdata0.020.000.02
chromosome.plot0.110.000.11
getMatchedSets30.90 0.2631.43
getSummary0.020.000.04
getWaldTest0.010.000.01
printEffects0.240.000.24
recode.geno000
snp.effects0.220.000.21
snp.list000
snp.logistic0.390.000.39
snp.matched25.02 0.0225.38
snp.scan.logistic0.010.000.01