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BioC 3.2: CHECK report for HIBAG on linux1.bioconductor.org

This page was generated on 2015-10-27 17:27:00 -0400 (Tue, 27 Oct 2015).

Package 491/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HIBAG 1.6.0
Xiuwen Zheng
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/HIBAG
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: HIBAG
Version: 1.6.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings HIBAG_1.6.0.tar.gz
StartedAt: 2015-10-27 04:37:37 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 04:38:40 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 63.0 seconds
RetCode: 0
Status:  OK 
CheckDir: HIBAG.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings HIBAG_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/HIBAG.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.6.0’
* 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 ... [8s/8s] 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 ... [9s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [23s/24s]
 [23s/24s] 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
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c HIBAG.cpp -o HIBAG.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c LibHLA.cpp -o LibHLA.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o HIBAG.so HIBAG.o LibHLA.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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-package0.9620.0120.974
hlaAllele0.0150.0000.015
hlaAlleleDigit0.0190.0000.019
hlaAlleleSubset0.0170.0000.017
hlaAttrBagging0.8240.0040.828
hlaBED2Geno0.2160.0080.224
hlaCheckSNPs0.0980.0000.098
hlaClose0.0930.0000.093
hlaCombineAllele0.0250.0000.025
hlaCombineModelObj0.4380.0000.438
hlaCompareAllele0.4160.0000.416
hlaErrMsg000
hlaFlankingSNP0.0090.0000.009
hlaGDS2Geno0.0620.0040.066
hlaGeno2PED0.0260.0000.026
hlaGenoAFreq0.0010.0000.004
hlaGenoCombine0.0790.0010.079
hlaGenoLD0.6460.0000.646
hlaGenoMFreq0.0060.0000.006
hlaGenoMRate0.0060.0000.006
hlaGenoMRate_Samp0.0080.0000.007
hlaGenoSubset0.0100.0000.009
hlaGenoSwitchStrand0.1230.0000.124
hlaLociInfo0.0050.0000.005
hlaMakeSNPGeno0.0220.0000.022
hlaModelFiles0.2860.0000.286
hlaModelFromObj0.1010.0000.101
hlaOutOfBag0.580.000.58
hlaParallelAttrBagging0.1360.0141.387
hlaPredMerge0.7630.0120.775
hlaPublish0.6040.0040.607
hlaReport0.6560.0040.660
hlaSNPID0.0070.0000.006
hlaSampleAllele0.0090.0000.010
hlaSplitAllele0.0490.0000.049
hlaSubModelObj0.0980.0000.097
hlaUniqueAllele0.0040.0040.008
plot.hlaAttrBagObj0.1960.0040.199
predict.hlaAttrBagClass0.6460.0000.645
print.hlaAttrBagClass0.1090.0000.110
summary.hlaAlleleClass0.0040.0000.005
summary.hlaSNPGenoClass0.0030.0000.003