Package: inveRsion

Version: 1.6.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings inveRsion_1.6.0.tar.gz

StartedAt: 2013-03-25 02:22:48 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:23:21 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 32.8 seconds

RetCode: 0

Status:  OK

CheckDir: inveRsion.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/inveRsion.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘inveRsion/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘inveRsion’ version ‘1.6.0’
* 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 ‘inveRsion’ can be installed ... OK
* checking installed package size ... 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 for left-over 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 ... 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 ... OK
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... 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

* installing *source* package ‘inveRsion’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init_inveRsion.c -o init_inveRsion.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c inversionModel.c -o inversionModel.o
inversionModel.c: In function ‘blockAndLev’:
inversionModel.c:185:9: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
inversionModel.c:167:8: warning: unused variable ‘ncol’ [-Wunused-variable]
inversionModel.c: In function ‘inversionModel’:
inversionModel.c:316:4: warning: "/*" within comment [-Wcomment]
inversionModel.c:360:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
inversionModel.c:237:26: warning: unused variable ‘i’ [-Wunused-variable]
inversionModel.c:237:8: warning: unused variable ‘ncol’ [-Wunused-variable]
inversionModel.c:459:13: warning: ‘LoglikeInv’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c writeGenoDat.c -o writeGenoDat.o
writeGenoDat.c: In function ‘writeGenoDat’:
writeGenoDat.c:36:20: warning: unused variable ‘fm’ [-Wunused-variable]
writeGenoDat.c:36:15: warning: unused variable ‘fa’ [-Wunused-variable]
writeGenoDat.c:34:16: warning: ‘dat’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/usr/local/lib64 -o inveRsion.so init_inveRsion.o inversionModel.o writeGenoDat.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/inveRsion.Rcheck/inveRsion/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘inveRsion’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘inveRsion.Rnw’ 
** testing if installed package can be loaded

* DONE (inveRsion)

name	user	system	elapsed
GenoDat-class	0.084	0.000	0.083
GenoDatROI-class	0.016	0.000	0.016
HaploCode-class	0.140	0.004	0.266
ac	0.004	0.000	0.016
accBic	2.112	0.000	2.366
accuracy-class	0.004	0.000	0.017
codeHaplo	0.08	0.00	0.10
gDat	0.008	0.000	0.006
getClassif-methods	0.224	0.000	0.227
getInv-methods	0.000	0.004	0.003
getROIs-methods	0.000	0.000	0.003
hapCode	0.008	0.004	0.013
invList	0.004	0.000	0.004
inveRsion-package	0	0	0
inversionList-class	0.004	0.000	0.003
listInv-methods	0.704	0.020	0.753
scan-class	0.016	0.000	0.016
scanInv	0.120	0.000	0.118
scanRes	0.008	0.000	0.024
setUpGenoDatFile	0.012	0.000	0.021