BioC 3.4: CHECK report for HIBAG on morelia

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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_1.9.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/HIBAG.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.9.3’
* 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 -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c HIBAG.cpp -o HIBAG.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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-3.4-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	0.716	0.013	0.744
hlaAllele	0.009	0.000	0.010
hlaAlleleDigit	0.010	0.001	0.010
hlaAlleleSubset	0.010	0.002	0.012
hlaAssocTest	0.866	0.016	0.882
hlaAttrBagging	0.477	0.009	0.488
hlaBED2Geno	0.154	0.008	0.161
hlaCheckAllele	0.001	0.000	0.001
hlaCheckSNPs	0.043	0.001	0.044
hlaCombineAllele	0.014	0.001	0.015
hlaCombineModelObj	0.197	0.001	0.198
hlaCompareAllele	0.360	0.005	0.364
hlaConvSequence	2.909	0.112	3.022
hlaErrMsg	0	0	0
hlaFlankingSNP	0.011	0.001	0.011
hlaGDS2Geno	0.082	0.004	0.086
hlaGeno2PED	0.033	0.002	0.035
hlaGenoAFreq	0.003	0.000	0.004
hlaGenoCombine	0.089	0.005	0.093
hlaGenoLD	0.688	0.002	0.690
hlaGenoMFreq	0.003	0.000	0.003
hlaGenoMRate	0.007	0.000	0.007
hlaGenoMRate_Samp	0.004	0.000	0.003
hlaGenoSubset	0.008	0.001	0.009
hlaGenoSwitchStrand	0.089	0.002	0.091
hlaLociInfo	0.003	0.000	0.003
hlaMakeSNPGeno	0.015	0.001	0.017
hlaModelFiles	0.208	0.003	0.212
hlaModelFromObj	0.068	0.001	0.069
hlaOutOfBag	0.541	0.007	0.548
hlaParallelAttrBagging	0.134	0.012	1.375
hlaPredMerge	0.373	0.003	0.376
hlaPublish	0.362	0.002	0.364
hlaReport	0.511	0.006	0.517
hlaSNPID	0.004	0.000	0.005
hlaSampleAllele	0.008	0.001	0.010
hlaSplitAllele	0.047	0.001	0.048
hlaSubModelObj	0.069	0.001	0.071
hlaUniqueAllele	0.012	0.001	0.013
plot.hlaAttrBagObj	0.127	0.002	0.130
predict.hlaAttrBagClass	0.364	0.004	0.368
print.hlaAttrBagClass	0.082	0.000	0.083
summary.hlaSNPGenoClass	0.002	0.001	0.002

BioC 3.4: CHECK report for HIBAG on morelia

Summary

Command output