BioC 3.1: CHECK report for HIBAG on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings HIBAG_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/HIBAG.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.4.0’
* 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/11s] 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 ... [7s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [12s/16s]
 [12s/16s] 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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c HIBAG.cpp -o HIBAG.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c LibHLA.cpp -o LibHLA.o
g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o HIBAG.so HIBAG.o LibHLA.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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	0.672	0.003	0.914
hlaAllele	0.008	0.000	0.009
hlaAlleleDigit	0.012	0.000	0.016
hlaAlleleSubset	0.008	0.004	0.012
hlaAttrBagging	0.564	0.008	0.856
hlaBED2Geno	0.059	0.000	0.069
hlaCheckSNPs	0.070	0.000	0.137
hlaClose	0.062	0.004	0.066
hlaCombineAllele	0.018	0.000	0.018
hlaCombineModelObj	0.308	0.000	0.354
hlaCompareAllele	0.499	0.012	0.644
hlaErrMsg	0.000	0.000	0.001
hlaFlankingSNP	0.007	0.000	0.007
hlaGDS2Geno	0.048	0.004	0.051
hlaGeno2PED	0.033	0.000	0.033
hlaGenoAFreq	0.006	0.000	0.007
hlaGenoCombine	0.060	0.000	0.108
hlaGenoLD	0.767	0.001	1.274
hlaGenoMFreq	0.005	0.000	0.004
hlaGenoMRate	0.005	0.003	0.018
hlaGenoMRate_Samp	0.002	0.000	0.004
hlaGenoSubset	0.008	0.000	0.024
hlaGenoSwitchStrand	0.084	0.000	0.101
hlaLociInfo	0.000	0.004	0.004
hlaMakeSNPGeno	0.039	0.004	0.066
hlaModelFiles	0.196	0.000	0.356
hlaModelFromObj	0.067	0.000	0.119
hlaOutOfBag	0.542	0.000	0.893
hlaParallelAttrBagging	0.124	0.009	2.410
hlaPredMerge	0.528	0.000	1.045
hlaPublish	0.535	0.004	0.956
hlaReport	0.509	0.000	0.575
hlaSNPID	0.005	0.000	0.005
hlaSampleAllele	0.006	0.000	0.007
hlaSplitAllele	0.035	0.000	0.034
hlaSubModelObj	0.065	0.000	0.067
hlaUniqueAllele	0.006	0.000	0.006
plot.hlaAttrBagObj	0.140	0.000	0.159
predict.hlaAttrBagClass	0.508	0.000	0.580
print.hlaAttrBagClass	0.133	0.000	0.166
summary.hlaAlleleClass	0.006	0.000	0.006
summary.hlaSNPGenoClass	0.003	0.000	0.015

BioC 3.1: CHECK report for HIBAG on zin2

Summary

Command output