BioC 3.5: CHECK report for HIBAG on veracruz2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HIBAG_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/HIBAG.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.0’
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c HIBAG.cpp -o HIBAG.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c LibHLA.cpp -o LibHLA.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o HIBAG.so HIBAG.o LibHLA.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/HIBAG.Rcheck/HIBAG/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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	0.599	0.019	0.634
hlaAllele	0.012	0.001	0.013
hlaAlleleDigit	0.013	0.002	0.015
hlaAlleleSubset	0.014	0.002	0.017
hlaAssocTest	1.017	0.020	1.078
hlaAttrBagging	0.563	0.012	0.596
hlaBED2Geno	0.185	0.009	0.204
hlaCheckAllele	0	0	0
hlaCheckSNPs	0.058	0.001	0.060
hlaCombineAllele	0.020	0.001	0.022
hlaCombineModelObj	0.247	0.002	0.254
hlaCompareAllele	0.371	0.008	0.384
hlaConvSequence	3.240	0.122	3.460
hlaErrMsg	0.000	0.001	0.001
hlaFlankingSNP	0.008	0.000	0.008
hlaGDS2Geno	0.080	0.004	0.086
hlaGeno2PED	0.034	0.002	0.044
hlaGenoAFreq	0.005	0.001	0.005
hlaGenoCombine	0.081	0.003	0.087
hlaGenoLD	0.742	0.007	0.765
hlaGenoMFreq	0.005	0.001	0.006
hlaGenoMRate	0.005	0.000	0.006
hlaGenoMRate_Samp	0.005	0.001	0.005
hlaGenoSubset	0.008	0.001	0.010
hlaGenoSwitchStrand	0.073	0.002	0.077
hlaLociInfo	0.004	0.000	0.006
hlaMakeSNPGeno	0.022	0.000	0.023
hlaModelFiles	0.181	0.004	0.189
hlaModelFromObj	0.059	0.001	0.060
hlaOutOfBag	0.490	0.007	0.512
hlaParallelAttrBagging	0.118	0.014	1.463
hlaPredMerge	0.492	0.004	0.503
hlaPublish	0.514	0.007	0.545
hlaReport	0.490	0.007	0.509
hlaSNPID	0.005	0.000	0.005
hlaSampleAllele	0.007	0.001	0.008
hlaSplitAllele	0.036	0.001	0.036
hlaSubModelObj	0.056	0.002	0.059
hlaUniqueAllele	0.007	0.000	0.007
plot.hlaAttrBagObj	0.140	0.003	0.150
predict.hlaAttrBagClass	0.482	0.007	0.503
print.hlaAttrBagClass	0.117	0.001	0.121
summary.hlaSNPGenoClass	0.003	0.001	0.003

BioC 3.5: CHECK report for HIBAG on veracruz2

Summary

Command output