BioC 3.3: CHECK report for HIBAG on oaxaca

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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_1.8.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-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 ‘1.8.3’
* 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-3.3-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	0.771	0.016	0.789
hlaAllele	0.014	0.001	0.015
hlaAlleleDigit	0.018	0.001	0.019
hlaAlleleSubset	0.017	0.002	0.019
hlaAssocTest	1.194	0.020	1.354
hlaAttrBagging	0.614	0.011	0.625
hlaBED2Geno	0.227	0.010	0.237
hlaCheckAllele	0.001	0.000	0.001
hlaCheckSNPs	0.066	0.001	0.067
hlaCombineAllele	0.024	0.001	0.024
hlaCombineModelObj	0.299	0.001	0.301
hlaCompareAllele	0.533	0.007	0.541
hlaConvSequence	3.785	0.134	4.454
hlaErrMsg	0.001	0.000	0.001
hlaFlankingSNP	0.010	0.001	0.010
hlaGDS2Geno	0.095	0.003	0.098
hlaGeno2PED	0.045	0.002	0.047
hlaGenoAFreq	0.006	0.001	0.006
hlaGenoCombine	0.085	0.004	0.089
hlaGenoLD	0.758	0.003	0.762
hlaGenoMFreq	0.010	0.001	0.011
hlaGenoMRate	0.006	0.000	0.006
hlaGenoMRate_Samp	0.004	0.000	0.005
hlaGenoSubset	0.011	0.000	0.012
hlaGenoSwitchStrand	0.123	0.002	0.125
hlaLociInfo	0.005	0.001	0.006
hlaMakeSNPGeno	0.016	0.001	0.017
hlaModelFiles	0.191	0.003	0.194
hlaModelFromObj	0.062	0.001	0.063
hlaOutOfBag	0.549	0.005	0.554
hlaParallelAttrBagging	0.151	0.015	1.439
hlaPredMerge	0.533	0.004	0.536
hlaPublish	0.542	0.004	0.547
hlaReport	0.549	0.005	0.554
hlaSNPID	0.004	0.000	0.005
hlaSampleAllele	0.009	0.000	0.010
hlaSplitAllele	0.048	0.001	0.050
hlaSubModelObj	0.072	0.002	0.074
hlaUniqueAllele	0.011	0.000	0.012
plot.hlaAttrBagObj	0.138	0.002	0.142
predict.hlaAttrBagClass	0.543	0.006	0.549
print.hlaAttrBagClass	0.126	0.001	0.127
summary.hlaSNPGenoClass	0.004	0.001	0.004

BioC 3.3: CHECK report for HIBAG on oaxaca

Summary

Command output