BioC 3.6: CHECK report for HIBAG on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings HIBAG_1.13.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/HIBAG.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.13.2’
* 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 ... NOTE
hlaReportPlot: no visible binding for global variable ‘dataset’
hlaReportPlot: no visible binding for global variable ‘matching’
Undefined global functions or variables:
  dataset matching
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/HIBAG.Rcheck/00check.log’
for details.

* installing *source* package ‘HIBAG’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c HIBAG.cpp -o HIBAG.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c LibHLA.cpp -o LibHLA.o
LibHLA.cpp: In member function ‘void HLA_LIB::CHaplotypeList::EraseDoubleHaplos(double, HLA_LIB::CHaplotypeList&) const’:
LibHLA.cpp:454:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (ss != OutHaplos.Num_Haplo)
         ^
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o HIBAG.so HIBAG.o LibHLA.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	0.552	0.000	0.552
hlaAllele	0.012	0.000	0.009
hlaAlleleDigit	0.012	0.000	0.012
hlaAlleleSubset	0.008	0.000	0.008
hlaAssocTest	0.720	0.008	0.731
hlaAttrBagging	0.444	0.000	0.444
hlaBED2Geno	0.160	0.000	0.161
hlaCheckAllele	0	0	0
hlaCheckSNPs	0.056	0.000	0.058
hlaCombineAllele	0.016	0.000	0.013
hlaCombineModelObj	0.236	0.000	0.236
hlaCompareAllele	0.392	0.000	0.395
hlaConvSequence	2.420	0.028	2.452
hlaErrMsg	0	0	0
hlaFlankingSNP	0.008	0.000	0.007
hlaGDS2Geno	0.084	0.004	0.087
hlaGeno2PED	0.076	0.004	0.081
hlaGenoAFreq	0.004	0.000	0.004
hlaGenoCombine	0.044	0.000	0.046
hlaGenoLD	0.480	0.000	0.479
hlaGenoMFreq	0.004	0.000	0.004
hlaGenoMRate	0.008	0.000	0.008
hlaGenoMRate_Samp	0.004	0.000	0.004
hlaGenoSubset	0.008	0.000	0.006
hlaGenoSwitchStrand	0.056	0.000	0.056
hlaLociInfo	0.004	0.000	0.003
hlaMakeSNPGeno	0.016	0.000	0.016
hlaModelFiles	0.168	0.000	0.168
hlaModelFromObj	0.060	0.000	0.057
hlaOutOfBag	0.544	0.004	0.548
hlaParallelAttrBagging	0.156	0.036	1.515
hlaPredMerge	0.416	0.000	0.416
hlaPublish	0.404	0.004	0.408
hlaReport	0.384	0.004	0.390
hlaReportPlot	2.752	0.032	2.782
hlaSNPID	0.004	0.000	0.004
hlaSampleAllele	0.004	0.000	0.006
hlaSplitAllele	0.032	0.000	0.032
hlaSubModelObj	0.056	0.000	0.056
hlaUniqueAllele	0.004	0.000	0.005
plot.hlaAttrBagObj	0.120	0.000	0.117
predict.hlaAttrBagClass	0.384	0.000	0.387
print.hlaAttrBagClass	0.104	0.000	0.104
summary.hlaSNPGenoClass	0.000	0.000	0.003

BioC 3.6: CHECK report for HIBAG on malbec1

Summary

Command output