BioC 3.2: 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/HIBAG.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.6.0’
* 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 ... [6s/6s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [21s/22s]
 [21s/23s] 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-3.2-bioc/meat/HIBAG.Rcheck/HIBAG/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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	0.786	0.016	0.802
hlaAllele	0.015	0.001	0.016
hlaAlleleDigit	0.017	0.001	0.018
hlaAlleleSubset	0.018	0.003	0.021
hlaAttrBagging	0.630	0.013	0.644
hlaBED2Geno	0.238	0.014	0.252
hlaCheckSNPs	0.058	0.001	0.059
hlaClose	0.060	0.001	0.061
hlaCombineAllele	0.022	0.002	0.024
hlaCombineModelObj	0.273	0.002	0.275
hlaCompareAllele	0.488	0.005	0.493
hlaErrMsg	0	0	0
hlaFlankingSNP	0.011	0.001	0.011
hlaGDS2Geno	0.067	0.005	0.072
hlaGeno2PED	0.030	0.002	0.032
hlaGenoAFreq	0.01	0.00	0.01
hlaGenoCombine	0.082	0.002	0.083
hlaGenoLD	0.755	0.003	0.758
hlaGenoMFreq	0.006	0.001	0.006
hlaGenoMRate	0.009	0.000	0.009
hlaGenoMRate_Samp	0.006	0.000	0.006
hlaGenoSubset	0.013	0.002	0.017
hlaGenoSwitchStrand	0.069	0.002	0.070
hlaLociInfo	0.005	0.000	0.005
hlaMakeSNPGeno	0.017	0.000	0.017
hlaModelFiles	0.179	0.002	0.181
hlaModelFromObj	0.059	0.001	0.059
hlaOutOfBag	0.454	0.006	0.461
hlaParallelAttrBagging	0.150	0.014	1.593
hlaPredMerge	0.539	0.004	0.544
hlaPublish	0.566	0.005	0.574
hlaReport	0.588	0.006	0.598
hlaSNPID	0.005	0.000	0.005
hlaSampleAllele	0.011	0.001	0.011
hlaSplitAllele	0.051	0.001	0.052
hlaSubModelObj	0.076	0.001	0.078
hlaUniqueAllele	0.005	0.000	0.005
plot.hlaAttrBagObj	0.142	0.002	0.145
predict.hlaAttrBagClass	0.548	0.006	0.555
print.hlaAttrBagClass	0.131	0.001	0.132
summary.hlaAlleleClass	0.009	0.001	0.009
summary.hlaSNPGenoClass	0.004	0.000	0.004

BioC 3.2: CHECK report for HIBAG on oaxaca

Summary

Command output