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BioC 3.1: CHECK report for HIBAG on morelia

This page was generated on 2015-10-09 09:42:39 -0700 (Fri, 09 Oct 2015).

Package 462/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HIBAG 1.4.0
Xiuwen Zheng
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/HIBAG
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: HIBAG
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HIBAG_1.4.0.tar.gz
StartedAt: 2015-10-09 02:58:35 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:59:30 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 54.4 seconds
RetCode: 0
Status:  OK 
CheckDir: HIBAG.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HIBAG_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/HIBAG.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.0’
* 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 ... [6s/6s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [11s/11s]
 [12s/12s] 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 -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c HIBAG.cpp -o HIBAG.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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-3.1-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)

HIBAG.Rcheck/HIBAG-Ex.timings:

nameusersystemelapsed
HIBAG-package0.5740.0260.600
hlaAllele0.0070.0010.007
hlaAlleleDigit0.0110.0010.012
hlaAlleleSubset0.0100.0010.011
hlaAttrBagging0.4760.0070.483
hlaBED2Geno0.0790.0020.082
hlaCheckSNPs0.0480.0000.048
hlaClose0.0410.0010.041
hlaCombineAllele0.0210.0020.023
hlaCombineModelObj0.2650.0340.300
hlaCompareAllele0.4410.0220.464
hlaErrMsg0.0000.0000.001
hlaFlankingSNP0.0060.0000.006
hlaGDS2Geno0.0450.0030.068
hlaGeno2PED0.0530.0020.055
hlaGenoAFreq0.0090.0010.010
hlaGenoCombine0.0630.0010.064
hlaGenoLD0.6840.0250.710
hlaGenoMFreq0.0050.0000.006
hlaGenoMRate0.0040.0000.003
hlaGenoMRate_Samp0.0050.0000.005
hlaGenoSubset0.0070.0010.007
hlaGenoSwitchStrand0.0950.0020.098
hlaLociInfo0.0050.0010.006
hlaMakeSNPGeno0.0430.0010.045
hlaModelFiles0.1310.0020.132
hlaModelFromObj0.0410.0000.042
hlaOutOfBag0.5310.0200.551
hlaParallelAttrBagging0.1560.0321.423
hlaPredMerge0.4270.0030.429
hlaPublish0.4820.0250.508
hlaReport0.4550.0450.501
hlaSNPID0.0030.0010.005
hlaSampleAllele0.0070.0030.010
hlaSplitAllele0.0510.0030.054
hlaSubModelObj0.0590.0010.059
hlaUniqueAllele0.0050.0000.005
plot.hlaAttrBagObj0.0900.0010.094
predict.hlaAttrBagClass0.4460.0050.452
print.hlaAttrBagClass0.1170.0140.132
summary.hlaAlleleClass0.0080.0010.008
summary.hlaSNPGenoClass0.0040.0000.005