BioC 3.4: CHECK report for HIBAG on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings HIBAG_1.9.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/HIBAG.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.9.3’
* 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
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c HIBAG.cpp -o HIBAG.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c LibHLA.cpp -o LibHLA.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o HIBAG.so HIBAG.o LibHLA.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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	0.680	0.012	0.689
hlaAllele	0.004	0.004	0.010
hlaAlleleDigit	0.012	0.000	0.011
hlaAlleleSubset	0.012	0.000	0.011
hlaAssocTest	0.800	0.000	0.799
hlaAttrBagging	0.592	0.000	0.590
hlaBED2Geno	0.144	0.000	0.143
hlaCheckAllele	0	0	0
hlaCheckSNPs	0.092	0.000	0.090
hlaCombineAllele	0.012	0.004	0.014
hlaCombineModelObj	0.340	0.000	0.342
hlaCompareAllele	0.520	0.004	0.524
hlaConvSequence	2.660	0.040	2.703
hlaErrMsg	0.000	0.000	0.001
hlaFlankingSNP	0.008	0.000	0.006
hlaGDS2Geno	0.116	0.000	0.117
hlaGeno2PED	0.024	0.000	0.024
hlaGenoAFreq	0.000	0.000	0.004
hlaGenoCombine	0.044	0.000	0.045
hlaGenoLD	0.540	0.004	0.541
hlaGenoMFreq	0.004	0.000	0.004
hlaGenoMRate	0.004	0.000	0.003
hlaGenoMRate_Samp	0.004	0.000	0.003
hlaGenoSubset	0.008	0.000	0.009
hlaGenoSwitchStrand	0.044	0.004	0.046
hlaLociInfo	0.004	0.000	0.003
hlaMakeSNPGeno	0.016	0.000	0.016
hlaModelFiles	0.216	0.000	0.215
hlaModelFromObj	0.088	0.000	0.088
hlaOutOfBag	0.608	0.000	0.606
hlaParallelAttrBagging	0.124	0.024	1.178
hlaPredMerge	0.540	0.008	0.554
hlaPublish	0.532	0.000	0.532
hlaReport	0.520	0.004	0.526
hlaSNPID	0.004	0.000	0.004
hlaSampleAllele	0.004	0.000	0.006
hlaSplitAllele	0.032	0.000	0.033
hlaSubModelObj	0.068	0.004	0.074
hlaUniqueAllele	0.004	0.000	0.005
plot.hlaAttrBagObj	0.160	0.000	0.158
predict.hlaAttrBagClass	0.544	0.004	0.549
print.hlaAttrBagClass	0.148	0.000	0.149
summary.hlaSNPGenoClass	0.004	0.000	0.003

BioC 3.4: CHECK report for HIBAG on zin1

Summary

Command output