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BioC 3.5: CHECK report for HIBAG on malbec2

This page was generated on 2017-08-16 13:16:24 -0400 (Wed, 16 Aug 2017).

Package 625/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HIBAG 1.12.0
Xiuwen Zheng
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/HIBAG
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -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: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings HIBAG_1.12.0.tar.gz
StartedAt: 2017-08-15 23:48:32 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:49:40 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 68.2 seconds
RetCode: 0
Status:  OK 
CheckDir: HIBAG.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings HIBAG_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/HIBAG.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.12.0’
* 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
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c HIBAG.cpp -o HIBAG.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c LibHLA.cpp -o LibHLA.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o HIBAG.so HIBAG.o LibHLA.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/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-package0.7200.0080.730
hlaAllele0.0080.0000.008
hlaAlleleDigit0.0040.0040.010
hlaAlleleSubset0.0120.0000.011
hlaAssocTest0.7320.0120.744
hlaAttrBagging0.4720.0000.473
hlaBED2Geno0.1560.0080.164
hlaCheckAllele0.0000.0000.001
hlaCheckSNPs0.0560.0000.056
hlaCombineAllele0.0120.0000.012
hlaCombineModelObj0.2600.0000.258
hlaCompareAllele0.4200.0080.428
hlaConvSequence2.3240.0442.371
hlaErrMsg0.0040.0000.000
hlaFlankingSNP0.0040.0000.006
hlaGDS2Geno0.0840.0040.087
hlaGeno2PED0.0800.0000.079
hlaGenoAFreq0.0040.0000.004
hlaGenoCombine0.0480.0000.050
hlaGenoLD0.4840.0040.486
hlaGenoMFreq0.0040.0000.004
hlaGenoMRate0.0080.0000.006
hlaGenoMRate_Samp0.0040.0000.004
hlaGenoSubset0.0080.0000.006
hlaGenoSwitchStrand0.0520.0000.055
hlaLociInfo0.0000.0000.003
hlaMakeSNPGeno0.0120.0000.015
hlaModelFiles0.1640.0000.164
hlaModelFromObj0.0520.0000.056
hlaOutOfBag0.4320.0000.434
hlaParallelAttrBagging0.1360.0161.299
hlaPredMerge0.4880.0040.493
hlaPublish0.5160.0040.519
hlaReport0.4160.0000.417
hlaSNPID0.0040.0000.005
hlaSampleAllele0.0080.0000.005
hlaSplitAllele0.0280.0000.028
hlaSubModelObj0.0560.0000.054
hlaUniqueAllele0.0000.0040.005
plot.hlaAttrBagObj0.1400.0000.138
predict.hlaAttrBagClass0.4080.0040.410
print.hlaAttrBagClass0.1120.0000.110
summary.hlaSNPGenoClass0.0000.0000.003