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BioC 3.5: CHECK report for HIBAG on veracruz2

This page was generated on 2017-10-18 14:32:54 -0400 (Wed, 18 Oct 2017).

Package 625/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HIBAG 1.12.0
Xiuwen Zheng
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/HIBAG
Branch: RELEASE_3_5
Last Commit: 20123b1
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: HIBAG
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HIBAG_1.12.0.tar.gz
StartedAt: 2017-10-18 04:48:57 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 04:50:18 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 80.7 seconds
RetCode: 0
Status:  OK 
CheckDir: HIBAG.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HIBAG_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/HIBAG.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.12.0’
* 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 ... 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

HIBAG.Rcheck/00install.out:

* 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-3.5-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)

HIBAG.Rcheck/HIBAG-Ex.timings:

nameusersystemelapsed
HIBAG-package0.5990.0190.634
hlaAllele0.0120.0010.013
hlaAlleleDigit0.0130.0020.015
hlaAlleleSubset0.0140.0020.017
hlaAssocTest1.0170.0201.078
hlaAttrBagging0.5630.0120.596
hlaBED2Geno0.1850.0090.204
hlaCheckAllele000
hlaCheckSNPs0.0580.0010.060
hlaCombineAllele0.0200.0010.022
hlaCombineModelObj0.2470.0020.254
hlaCompareAllele0.3710.0080.384
hlaConvSequence3.2400.1223.460
hlaErrMsg0.0000.0010.001
hlaFlankingSNP0.0080.0000.008
hlaGDS2Geno0.0800.0040.086
hlaGeno2PED0.0340.0020.044
hlaGenoAFreq0.0050.0010.005
hlaGenoCombine0.0810.0030.087
hlaGenoLD0.7420.0070.765
hlaGenoMFreq0.0050.0010.006
hlaGenoMRate0.0050.0000.006
hlaGenoMRate_Samp0.0050.0010.005
hlaGenoSubset0.0080.0010.010
hlaGenoSwitchStrand0.0730.0020.077
hlaLociInfo0.0040.0000.006
hlaMakeSNPGeno0.0220.0000.023
hlaModelFiles0.1810.0040.189
hlaModelFromObj0.0590.0010.060
hlaOutOfBag0.4900.0070.512
hlaParallelAttrBagging0.1180.0141.463
hlaPredMerge0.4920.0040.503
hlaPublish0.5140.0070.545
hlaReport0.4900.0070.509
hlaSNPID0.0050.0000.005
hlaSampleAllele0.0070.0010.008
hlaSplitAllele0.0360.0010.036
hlaSubModelObj0.0560.0020.059
hlaUniqueAllele0.0070.0000.007
plot.hlaAttrBagObj0.1400.0030.150
predict.hlaAttrBagClass0.4820.0070.503
print.hlaAttrBagClass0.1170.0010.121
summary.hlaSNPGenoClass0.0030.0010.003