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).
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 | | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HIBAG_1.4.0.tar.gz
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* 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:
name | user | system | elapsed
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HIBAG-package | 1.325 | 0.026 | 1.352 |
|
hlaAllele | 0.015 | 0.001 | 0.016 |
|
hlaAlleleDigit | 0.029 | 0.002 | 0.031 |
|
hlaAlleleSubset | 0.024 | 0.004 | 0.028 |
|
hlaAttrBagging | 1.159 | 0.019 | 1.180 |
|
hlaBED2Geno | 0.120 | 0.006 | 0.127 |
|
hlaCheckSNPs | 0.133 | 0.001 | 0.135 |
|
hlaClose | 0.123 | 0.001 | 0.124 |
|
hlaCombineAllele | 0.042 | 0.002 | 0.043 |
|
hlaCombineModelObj | 0.617 | 0.003 | 0.621 |
|
hlaCompareAllele | 1.057 | 0.017 | 1.076 |
|
hlaErrMsg | 0.001 | 0.000 | 0.001 |
|
hlaFlankingSNP | 0.015 | 0.001 | 0.016 |
|
hlaGDS2Geno | 0.100 | 0.007 | 0.106 |
|
hlaGeno2PED | 0.065 | 0.003 | 0.069 |
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hlaGenoAFreq | 0.013 | 0.001 | 0.014 |
|
hlaGenoCombine | 0.108 | 0.008 | 0.117 |
|
hlaGenoLD | 1.328 | 0.007 | 1.336 |
|
hlaGenoMFreq | 0.008 | 0.000 | 0.009 |
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hlaGenoMRate | 0.009 | 0.000 | 0.009 |
|
hlaGenoMRate_Samp | 0.009 | 0.000 | 0.009 |
|
hlaGenoSubset | 0.018 | 0.001 | 0.019 |
|
hlaGenoSwitchStrand | 0.150 | 0.006 | 0.157 |
|
hlaLociInfo | 0.008 | 0.001 | 0.009 |
|
hlaMakeSNPGeno | 0.078 | 0.003 | 0.082 |
|
hlaModelFiles | 0.370 | 0.003 | 0.380 |
|
hlaModelFromObj | 0.122 | 0.001 | 0.124 |
|
hlaOutOfBag | 1.011 | 0.007 | 1.019 |
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hlaParallelAttrBagging | 0.222 | 0.019 | 2.858 |
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hlaPredMerge | 0.901 | 0.003 | 0.904 |
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hlaPublish | 1.003 | 0.005 | 1.007 |
|
hlaReport | 0.909 | 0.006 | 0.921 |
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hlaSNPID | 0.004 | 0.000 | 0.005 |
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hlaSampleAllele | 0.012 | 0.001 | 0.013 |
|
hlaSplitAllele | 0.063 | 0.000 | 0.064 |
|
hlaSubModelObj | 0.104 | 0.002 | 0.105 |
|
hlaUniqueAllele | 0.012 | 0.001 | 0.012 |
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plot.hlaAttrBagObj | 0.222 | 0.002 | 0.226 |
|
predict.hlaAttrBagClass | 0.910 | 0.007 | 0.918 |
|
print.hlaAttrBagClass | 0.229 | 0.002 | 0.231 |
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summary.hlaAlleleClass | 0.008 | 0.001 | 0.009 |
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summary.hlaSNPGenoClass | 0.007 | 0.000 | 0.007 |
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