BioC 3.5: CHECK report for HIBAG on veracruz2

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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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/HIBAG.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.0’
* 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   -fPIC  -Wall -g -O2  -c HIBAG.cpp -o HIBAG.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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	0.656	0.015	0.690
hlaAllele	0.013	0.001	0.015
hlaAlleleDigit	0.014	0.002	0.016
hlaAlleleSubset	0.012	0.001	0.014
hlaAssocTest	0.841	0.018	0.884
hlaAttrBagging	0.489	0.008	0.508
hlaBED2Geno	0.149	0.008	0.157
hlaCheckAllele	0.000	0.000	0.001
hlaCheckSNPs	0.054	0.001	0.056
hlaCombineAllele	0.020	0.001	0.020
hlaCombineModelObj	0.273	0.002	0.284
hlaCompareAllele	0.495	0.010	0.518
hlaConvSequence	3.298	0.119	3.519
hlaErrMsg	0.000	0.000	0.001
hlaFlankingSNP	0.009	0.001	0.009
hlaGDS2Geno	0.091	0.004	0.098
hlaGeno2PED	0.031	0.002	0.033
hlaGenoAFreq	0.004	0.001	0.005
hlaGenoCombine	0.085	0.004	0.099
hlaGenoLD	0.675	0.003	0.696
hlaGenoMFreq	0.003	0.000	0.004
hlaGenoMRate	0.004	0.000	0.004
hlaGenoMRate_Samp	0.009	0.001	0.012
hlaGenoSubset	0.008	0.001	0.009
hlaGenoSwitchStrand	0.114	0.002	0.116
hlaLociInfo	0.005	0.001	0.005
hlaMakeSNPGeno	0.020	0.001	0.023
hlaModelFiles	0.168	0.002	0.176
hlaModelFromObj	0.060	0.001	0.061
hlaOutOfBag	0.474	0.005	0.496
hlaParallelAttrBagging	0.116	0.013	1.479
hlaPredMerge	0.483	0.003	0.499
hlaPublish	0.521	0.004	0.546
hlaReport	0.449	0.005	0.465
hlaSNPID	0.003	0.000	0.003
hlaSampleAllele	0.006	0.000	0.007
hlaSplitAllele	0.037	0.001	0.038
hlaSubModelObj	0.060	0.001	0.061
hlaUniqueAllele	0.006	0.001	0.007
plot.hlaAttrBagObj	0.123	0.002	0.128
predict.hlaAttrBagClass	0.454	0.005	0.472
print.hlaAttrBagClass	0.105	0.002	0.112
summary.hlaSNPGenoClass	0.003	0.000	0.004

BioC 3.5: CHECK report for HIBAG on veracruz2

Summary

Command output