BioC 3.2: CHECK report for HIBAG on zin1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings HIBAG_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/HIBAG.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HIBAG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HIBAG’ 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HIBAG’ can be installed ... [8s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 loading without being on the library search path ... OK
* checking 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [20s/21s]
 [20s/22s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘HIBAG’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c HIBAG.cpp -o HIBAG.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c LibHLA.cpp -o LibHLA.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o HIBAG.so HIBAG.o LibHLA.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/HIBAG.Rcheck/HIBAG/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HIBAG)

name	user	system	elapsed
HIBAG-package	0.727	0.004	0.730
hlaAllele	0.011	0.000	0.011
hlaAlleleDigit	0.013	0.000	0.013
hlaAlleleSubset	0.005	0.008	0.013
hlaAttrBagging	0.610	0.004	0.613
hlaBED2Geno	0.168	0.000	0.168
hlaCheckSNPs	0.069	0.000	0.069
hlaClose	0.068	0.000	0.068
hlaCombineAllele	0.014	0.004	0.018
hlaCombineModelObj	0.307	0.000	0.307
hlaCompareAllele	0.506	0.012	0.517
hlaErrMsg	0.001	0.000	0.001
hlaFlankingSNP	0.008	0.000	0.007
hlaGDS2Geno	0.068	0.004	0.071
hlaGeno2PED	0.032	0.000	0.032
hlaGenoAFreq	0.008	0.000	0.008
hlaGenoCombine	0.051	0.000	0.051
hlaGenoLD	0.746	0.000	0.745
hlaGenoMFreq	0.005	0.000	0.005
hlaGenoMRate	0.006	0.000	0.007
hlaGenoMRate_Samp	0.005	0.000	0.004
hlaGenoSubset	0.009	0.000	0.012
hlaGenoSwitchStrand	0.044	0.008	0.052
hlaLociInfo	0.004	0.000	0.004
hlaMakeSNPGeno	0.017	0.000	0.017
hlaModelFiles	0.196	0.000	0.195
hlaModelFromObj	0.067	0.000	0.068
hlaOutOfBag	0.549	0.004	0.552
hlaParallelAttrBagging	0.163	0.008	1.289
hlaPredMerge	0.598	0.004	0.601
hlaPublish	0.559	0.000	0.559
hlaReport	0.509	0.000	0.508
hlaSNPID	0.005	0.000	0.004
hlaSampleAllele	0.006	0.000	0.006
hlaSplitAllele	0.033	0.000	0.033
hlaSubModelObj	0.07	0.00	0.07
hlaUniqueAllele	0.006	0.000	0.007
plot.hlaAttrBagObj	0.154	0.004	0.158
predict.hlaAttrBagClass	0.544	0.000	0.543
print.hlaAttrBagClass	0.133	0.000	0.132
summary.hlaAlleleClass	0.005	0.000	0.006
summary.hlaSNPGenoClass	0.003	0.000	0.003

BioC 3.2: CHECK report for HIBAG on zin1

Summary

Command output