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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/HIBAG.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.10.0’
* 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 -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	0.744	0.017	0.823
hlaAllele	0.019	0.001	0.022
hlaAlleleDigit	0.016	0.001	0.016
hlaAlleleSubset	0.015	0.002	0.018
hlaAssocTest	1.118	0.021	1.141
hlaAttrBagging	0.622	0.010	0.679
hlaBED2Geno	0.190	0.009	0.198
hlaCheckAllele	0.001	0.000	0.001
hlaCheckSNPs	0.046	0.000	0.047
hlaCombineAllele	0.024	0.001	0.024
hlaCombineModelObj	0.299	0.001	0.301
hlaCompareAllele	0.548	0.007	0.555
hlaConvSequence	3.693	0.136	3.839
hlaErrMsg	0.001	0.000	0.001
hlaFlankingSNP	0.010	0.001	0.011
hlaGDS2Geno	0.090	0.003	0.094
hlaGeno2PED	0.043	0.003	0.095
hlaGenoAFreq	0.004	0.000	0.005
hlaGenoCombine	0.075	0.003	0.079
hlaGenoLD	0.792	0.004	0.798
hlaGenoMFreq	0.005	0.001	0.006
hlaGenoMRate	0.006	0.000	0.006
hlaGenoMRate_Samp	0.010	0.001	0.011
hlaGenoSubset	0.006	0.001	0.007
hlaGenoSwitchStrand	0.078	0.002	0.081
hlaLociInfo	0.004	0.001	0.004
hlaMakeSNPGeno	0.025	0.000	0.025
hlaModelFiles	0.205	0.004	0.255
hlaModelFromObj	0.049	0.001	0.050
hlaOutOfBag	0.544	0.005	0.551
hlaParallelAttrBagging	0.158	0.014	1.402
hlaPredMerge	0.582	0.004	0.587
hlaPublish	0.559	0.004	0.563
hlaReport	0.544	0.005	0.550
hlaSNPID	0.005	0.000	0.005
hlaSampleAllele	0.009	0.000	0.010
hlaSplitAllele	0.052	0.000	0.053
hlaSubModelObj	0.066	0.002	0.067
hlaUniqueAllele	0.008	0.000	0.008
plot.hlaAttrBagObj	0.131	0.002	0.166
predict.hlaAttrBagClass	0.539	0.006	0.546
print.hlaAttrBagClass	0.131	0.001	0.133
summary.hlaSNPGenoClass	0.004	0.000	0.004

BioC 3.4: CHECK report for HIBAG on morelia

Summary

Command output