BioC 3.6: CHECK report for HIBAG on veracruz1

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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_1.13.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.13.2’
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/HIBAG.Rcheck/00check.log’
for details.

* 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-3.6-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	0.652	0.017	0.681
hlaAllele	0.016	0.001	0.017
hlaAlleleDigit	0.015	0.002	0.018
hlaAlleleSubset	0.016	0.002	0.018
hlaAssocTest	0.946	0.018	0.985
hlaAttrBagging	0.497	0.011	0.531
hlaBED2Geno	0.175	0.009	0.186
hlaCheckAllele	0.001	0.000	0.001
hlaCheckSNPs	0.063	0.002	0.065
hlaCombineAllele	0.020	0.001	0.020
hlaCombineModelObj	0.235	0.002	0.243
hlaCompareAllele	0.475	0.008	0.503
hlaConvSequence	3.567	0.114	3.788
hlaErrMsg	0.000	0.000	0.008
hlaFlankingSNP	0.009	0.001	0.010
hlaGDS2Geno	0.084	0.004	0.090
hlaGeno2PED	0.034	0.002	0.036
hlaGenoAFreq	0.005	0.001	0.006
hlaGenoCombine	0.081	0.002	0.084
hlaGenoLD	0.711	0.004	0.722
hlaGenoMFreq	0.005	0.000	0.004
hlaGenoMRate	0.009	0.000	0.009
hlaGenoMRate_Samp	0.005	0.001	0.005
hlaGenoSubset	0.011	0.001	0.012
hlaGenoSwitchStrand	0.120	0.002	0.126
hlaLociInfo	0.005	0.001	0.005
hlaMakeSNPGeno	0.020	0.000	0.021
hlaModelFiles	0.193	0.004	0.200
hlaModelFromObj	0.064	0.001	0.066
hlaOutOfBag	0.510	0.006	0.546
hlaParallelAttrBagging	0.148	0.014	1.545
hlaPredMerge	0.501	0.005	0.513
hlaPublish	0.502	0.005	0.531
hlaReport	0.497	0.005	0.521
hlaReportPlot	3.820	0.021	3.984
hlaSNPID	0.005	0.000	0.005
hlaSampleAllele	0.008	0.001	0.009
hlaSplitAllele	0.047	0.001	0.047
hlaSubModelObj	0.069	0.002	0.071
hlaUniqueAllele	0.007	0.000	0.007
plot.hlaAttrBagObj	0.145	0.002	0.154
predict.hlaAttrBagClass	0.497	0.006	0.529
print.hlaAttrBagClass	0.126	0.002	0.135
summary.hlaSNPGenoClass	0.004	0.001	0.003

BioC 3.6: CHECK report for HIBAG on veracruz1

Summary

Command output