BioC 3.2: CHECK report for HIBAG on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings HIBAG_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/HIBAG.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.5.0’
* 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 ... [8s/8s] 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’ [20s/22s]
 [21s/22s] 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
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c HIBAG.cpp -o HIBAG.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c LibHLA.cpp -o LibHLA.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o HIBAG.so HIBAG.o LibHLA.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/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	0.765	0.003	0.775
hlaAllele	0.009	0.004	0.012
hlaAlleleDigit	0.010	0.004	0.014
hlaAlleleSubset	0.015	0.000	0.015
hlaAttrBagging	0.592	0.000	0.595
hlaBED2Geno	0.164	0.000	0.163
hlaCheckSNPs	0.069	0.000	0.069
hlaClose	0.065	0.000	0.065
hlaCombineAllele	0.017	0.000	0.017
hlaCombineModelObj	0.307	0.000	0.307
hlaCompareAllele	0.504	0.012	0.516
hlaErrMsg	0.001	0.001	0.000
hlaFlankingSNP	0.007	0.000	0.008
hlaGDS2Geno	0.079	0.003	0.083
hlaGeno2PED	0.037	0.000	0.037
hlaGenoAFreq	0.008	0.004	0.009
hlaGenoCombine	0.089	0.001	0.090
hlaGenoLD	0.744	0.007	0.752
hlaGenoMFreq	0.005	0.000	0.004
hlaGenoMRate	0.004	0.000	0.005
hlaGenoMRate_Samp	0.006	0.000	0.006
hlaGenoSubset	0.007	0.000	0.007
hlaGenoSwitchStrand	0.082	0.007	0.089
hlaLociInfo	0.003	0.000	0.004
hlaMakeSNPGeno	0.015	0.001	0.014
hlaModelFiles	0.194	0.004	0.198
hlaModelFromObj	0.070	0.000	0.069
hlaOutOfBag	0.54	0.00	0.55
hlaParallelAttrBagging	0.132	0.018	1.322
hlaPredMerge	0.593	0.004	0.596
hlaPublish	0.546	0.000	0.546
hlaReport	0.51	0.00	0.51
hlaSNPID	0.005	0.000	0.004
hlaSampleAllele	0.006	0.000	0.007
hlaSplitAllele	0.032	0.000	0.036
hlaSubModelObj	0.066	0.000	0.066
hlaUniqueAllele	0.006	0.000	0.005
plot.hlaAttrBagObj	0.139	0.000	0.140
predict.hlaAttrBagClass	0.510	0.004	0.514
print.hlaAttrBagClass	0.132	0.000	0.132
summary.hlaAlleleClass	0.005	0.000	0.006
summary.hlaSNPGenoClass	0.003	0.000	0.004

BioC 3.2: CHECK report for HIBAG on zin1

Summary

Command output