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BioC 3.1: CHECK report for HIBAG on petty

This page was generated on 2015-10-09 09:37:18 -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: 2015-10-08 23:40:41 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:42:11 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 90.6 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 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [9s/10s] 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 ... [14s/16s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [23s/23s]
 [23s/23s] 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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c HIBAG.cpp -o HIBAG.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LibHLA.cpp -o LibHLA.o
llvm-g++-4.2 -arch x86_64 -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 -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-package1.3250.0261.352
hlaAllele0.0150.0010.016
hlaAlleleDigit0.0290.0020.031
hlaAlleleSubset0.0240.0040.028
hlaAttrBagging1.1590.0191.180
hlaBED2Geno0.1200.0060.127
hlaCheckSNPs0.1330.0010.135
hlaClose0.1230.0010.124
hlaCombineAllele0.0420.0020.043
hlaCombineModelObj0.6170.0030.621
hlaCompareAllele1.0570.0171.076
hlaErrMsg0.0010.0000.001
hlaFlankingSNP0.0150.0010.016
hlaGDS2Geno0.1000.0070.106
hlaGeno2PED0.0650.0030.069
hlaGenoAFreq0.0130.0010.014
hlaGenoCombine0.1080.0080.117
hlaGenoLD1.3280.0071.336
hlaGenoMFreq0.0080.0000.009
hlaGenoMRate0.0090.0000.009
hlaGenoMRate_Samp0.0090.0000.009
hlaGenoSubset0.0180.0010.019
hlaGenoSwitchStrand0.1500.0060.157
hlaLociInfo0.0080.0010.009
hlaMakeSNPGeno0.0780.0030.082
hlaModelFiles0.3700.0030.380
hlaModelFromObj0.1220.0010.124
hlaOutOfBag1.0110.0071.019
hlaParallelAttrBagging0.2220.0192.858
hlaPredMerge0.9010.0030.904
hlaPublish1.0030.0051.007
hlaReport0.9090.0060.921
hlaSNPID0.0040.0000.005
hlaSampleAllele0.0120.0010.013
hlaSplitAllele0.0630.0000.064
hlaSubModelObj0.1040.0020.105
hlaUniqueAllele0.0120.0010.012
plot.hlaAttrBagObj0.2220.0020.226
predict.hlaAttrBagClass0.9100.0070.918
print.hlaAttrBagClass0.2290.0020.231
summary.hlaAlleleClass0.0080.0010.009
summary.hlaSNPGenoClass0.0070.0000.007