BioC 3.2: CHECK report for HIBAG on perceval

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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 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [7s/7s] 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 ... [10s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [28s/30s]
 [29s/31s] 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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c HIBAG.cpp -o HIBAG.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LibHLA.cpp -o LibHLA.o
llvm-g++-4.2 -arch x86_64 -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 -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	0.947	0.018	0.965
hlaAllele	0.015	0.001	0.016
hlaAlleleDigit	0.018	0.002	0.020
hlaAlleleSubset	0.018	0.003	0.021
hlaAttrBagging	0.810	0.012	0.822
hlaBED2Geno	0.213	0.012	0.226
hlaCheckSNPs	0.090	0.001	0.092
hlaClose	0.084	0.001	0.086
hlaCombineAllele	0.025	0.001	0.026
hlaCombineModelObj	0.428	0.002	0.431
hlaCompareAllele	0.729	0.011	0.739
hlaErrMsg	0.000	0.000	0.001
hlaFlankingSNP	0.009	0.000	0.010
hlaGDS2Geno	0.096	0.006	0.102
hlaGeno2PED	0.036	0.003	0.038
hlaGenoAFreq	0.01	0.00	0.01
hlaGenoCombine	0.058	0.001	0.059
hlaGenoLD	0.998	0.006	1.005
hlaGenoMFreq	0.006	0.001	0.007
hlaGenoMRate	0.009	0.001	0.010
hlaGenoMRate_Samp	0.005	0.001	0.007
hlaGenoSubset	0.016	0.002	0.018
hlaGenoSwitchStrand	0.060	0.002	0.061
hlaLociInfo	0.005	0.001	0.005
hlaMakeSNPGeno	0.022	0.001	0.023
hlaModelFiles	0.269	0.003	0.272
hlaModelFromObj	0.086	0.001	0.087
hlaOutOfBag	0.743	0.005	0.748
hlaParallelAttrBagging	0.166	0.015	1.936
hlaPredMerge	0.762	0.004	0.766
hlaPublish	0.793	0.005	0.797
hlaReport	0.737	0.005	0.742
hlaSNPID	0.004	0.000	0.005
hlaSampleAllele	0.009	0.001	0.010
hlaSplitAllele	0.048	0.001	0.048
hlaSubModelObj	0.093	0.001	0.095
hlaUniqueAllele	0.009	0.000	0.009
plot.hlaAttrBagObj	0.194	0.003	0.198
predict.hlaAttrBagClass	0.733	0.006	0.738
print.hlaAttrBagClass	0.181	0.001	0.182
summary.hlaAlleleClass	0.007	0.001	0.007
summary.hlaSNPGenoClass	0.005	0.000	0.005

BioC 3.2: CHECK report for HIBAG on perceval

Summary

Command output