BioC 3.2: CHECK report for HIBAG on linux1.bioconductor.org

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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_1.6.0.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 ‘1.6.0’
* 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 ... [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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [23s/24s]
 [23s/24s] 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	0.962	0.012	0.974
hlaAllele	0.015	0.000	0.015
hlaAlleleDigit	0.019	0.000	0.019
hlaAlleleSubset	0.017	0.000	0.017
hlaAttrBagging	0.824	0.004	0.828
hlaBED2Geno	0.216	0.008	0.224
hlaCheckSNPs	0.098	0.000	0.098
hlaClose	0.093	0.000	0.093
hlaCombineAllele	0.025	0.000	0.025
hlaCombineModelObj	0.438	0.000	0.438
hlaCompareAllele	0.416	0.000	0.416
hlaErrMsg	0	0	0
hlaFlankingSNP	0.009	0.000	0.009
hlaGDS2Geno	0.062	0.004	0.066
hlaGeno2PED	0.026	0.000	0.026
hlaGenoAFreq	0.001	0.000	0.004
hlaGenoCombine	0.079	0.001	0.079
hlaGenoLD	0.646	0.000	0.646
hlaGenoMFreq	0.006	0.000	0.006
hlaGenoMRate	0.006	0.000	0.006
hlaGenoMRate_Samp	0.008	0.000	0.007
hlaGenoSubset	0.010	0.000	0.009
hlaGenoSwitchStrand	0.123	0.000	0.124
hlaLociInfo	0.005	0.000	0.005
hlaMakeSNPGeno	0.022	0.000	0.022
hlaModelFiles	0.286	0.000	0.286
hlaModelFromObj	0.101	0.000	0.101
hlaOutOfBag	0.58	0.00	0.58
hlaParallelAttrBagging	0.136	0.014	1.387
hlaPredMerge	0.763	0.012	0.775
hlaPublish	0.604	0.004	0.607
hlaReport	0.656	0.004	0.660
hlaSNPID	0.007	0.000	0.006
hlaSampleAllele	0.009	0.000	0.010
hlaSplitAllele	0.049	0.000	0.049
hlaSubModelObj	0.098	0.000	0.097
hlaUniqueAllele	0.004	0.004	0.008
plot.hlaAttrBagObj	0.196	0.004	0.199
predict.hlaAttrBagClass	0.646	0.000	0.645
print.hlaAttrBagClass	0.109	0.000	0.110
summary.hlaAlleleClass	0.004	0.000	0.005
summary.hlaSNPGenoClass	0.003	0.000	0.003

BioC 3.2: CHECK report for HIBAG on linux1.bioconductor.org

Summary

Command output