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BioC 3.4: CHECK report for HIBAG on morelia

This page was generated on 2017-04-15 16:26:15 -0400 (Sat, 15 Apr 2017).

Package 590/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HIBAG 1.10.0
Xiuwen Zheng
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/HIBAG
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  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: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HIBAG_1.10.0.tar.gz
StartedAt: 2017-04-15 03:35:41 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 03:37:21 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 100.2 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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/HIBAG.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.10.0’
* 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 -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-3.4-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-package0.7440.0170.823
hlaAllele0.0190.0010.022
hlaAlleleDigit0.0160.0010.016
hlaAlleleSubset0.0150.0020.018
hlaAssocTest1.1180.0211.141
hlaAttrBagging0.6220.0100.679
hlaBED2Geno0.1900.0090.198
hlaCheckAllele0.0010.0000.001
hlaCheckSNPs0.0460.0000.047
hlaCombineAllele0.0240.0010.024
hlaCombineModelObj0.2990.0010.301
hlaCompareAllele0.5480.0070.555
hlaConvSequence3.6930.1363.839
hlaErrMsg0.0010.0000.001
hlaFlankingSNP0.0100.0010.011
hlaGDS2Geno0.0900.0030.094
hlaGeno2PED0.0430.0030.095
hlaGenoAFreq0.0040.0000.005
hlaGenoCombine0.0750.0030.079
hlaGenoLD0.7920.0040.798
hlaGenoMFreq0.0050.0010.006
hlaGenoMRate0.0060.0000.006
hlaGenoMRate_Samp0.0100.0010.011
hlaGenoSubset0.0060.0010.007
hlaGenoSwitchStrand0.0780.0020.081
hlaLociInfo0.0040.0010.004
hlaMakeSNPGeno0.0250.0000.025
hlaModelFiles0.2050.0040.255
hlaModelFromObj0.0490.0010.050
hlaOutOfBag0.5440.0050.551
hlaParallelAttrBagging0.1580.0141.402
hlaPredMerge0.5820.0040.587
hlaPublish0.5590.0040.563
hlaReport0.5440.0050.550
hlaSNPID0.0050.0000.005
hlaSampleAllele0.0090.0000.010
hlaSplitAllele0.0520.0000.053
hlaSubModelObj0.0660.0020.067
hlaUniqueAllele0.0080.0000.008
plot.hlaAttrBagObj0.1310.0020.166
predict.hlaAttrBagClass0.5390.0060.546
print.hlaAttrBagClass0.1310.0010.133
summary.hlaSNPGenoClass0.0040.0000.004