BioC 3.5: CHECK report for HIBAG on toluca2

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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_1.11.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/HIBAG.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.11.1’
* 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-3.5-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	0.728	0.018	0.753
hlaAllele	0.014	0.001	0.015
hlaAlleleDigit	0.017	0.001	0.019
hlaAlleleSubset	0.017	0.002	0.019
hlaAssocTest	1.099	0.020	1.154
hlaAttrBagging	0.58	0.01	0.59
hlaBED2Geno	0.196	0.008	0.204
hlaCheckAllele	0.001	0.000	0.000
hlaCheckSNPs	0.063	0.001	0.064
hlaCombineAllele	0.022	0.001	0.023
hlaCombineModelObj	0.287	0.002	0.290
hlaCompareAllele	0.540	0.010	0.575
hlaConvSequence	3.780	0.146	4.005
hlaErrMsg	0.001	0.000	0.000
hlaFlankingSNP	0.010	0.001	0.010
hlaGDS2Geno	0.090	0.004	0.097
hlaGeno2PED	0.042	0.002	0.044
hlaGenoAFreq	0.005	0.000	0.006
hlaGenoCombine	0.088	0.003	0.092
hlaGenoLD	0.813	0.004	0.818
hlaGenoMFreq	0.005	0.000	0.005
hlaGenoMRate	0.005	0.001	0.005
hlaGenoMRate_Samp	0.01	0.00	0.01
hlaGenoSubset	0.008	0.001	0.009
hlaGenoSwitchStrand	0.134	0.002	0.137
hlaLociInfo	0.005	0.001	0.006
hlaMakeSNPGeno	0.023	0.001	0.023
hlaModelFiles	0.191	0.002	0.194
hlaModelFromObj	0.062	0.001	0.064
hlaOutOfBag	0.542	0.005	0.548
hlaParallelAttrBagging	0.137	0.012	1.609
hlaPredMerge	0.550	0.004	0.555
hlaPublish	0.562	0.004	0.570
hlaReport	0.523	0.005	0.533
hlaSNPID	0.004	0.001	0.004
hlaSampleAllele	0.009	0.000	0.009
hlaSplitAllele	0.051	0.001	0.053
hlaSubModelObj	0.067	0.001	0.070
hlaUniqueAllele	0.007	0.000	0.008
plot.hlaAttrBagObj	0.152	0.002	0.156
predict.hlaAttrBagClass	0.530	0.005	0.538
print.hlaAttrBagClass	0.132	0.002	0.134
summary.hlaSNPGenoClass	0.003	0.000	0.004

BioC 3.5: CHECK report for HIBAG on toluca2

Summary

Command output