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CHECK report for tigre on merida2

This page was generated on 2018-10-17 08:48:35 -0400 (Wed, 17 Oct 2018).

Package 1480/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tigre 1.34.0
Antti Honkela
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/tigre
Branch: RELEASE_3_7
Last Commit: 024adbf
Last Changed Date: 2018-04-30 10:35:13 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: tigre
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tigre.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tigre_1.34.0.tar.gz
StartedAt: 2018-10-17 00:24:11 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:26:27 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 136.4 seconds
RetCode: 0
Status:  OK 
CheckDir: tigre.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tigre.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tigre_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/tigre.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tigre/DESCRIPTION’ ... OK
* this is package ‘tigre’ version ‘1.34.0’
* 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 ‘tigre’ 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 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 ... NOTE
  Failed with error:  'package 'oligoClasses' could not be loaded'
  Error in .requirePackage(package) : 
    unable to find required package 'puma'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
processData 6.335  0.236   7.489
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/tigre.Rcheck/00check.log’
for details.



Installation output

tigre.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tigre
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘tigre’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c miscCFunctions.c -o miscCFunctions.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 tigre.so miscCFunctions.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/tigre/libs
** R
** data
** 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 (tigre)

Tests output


Example timings

tigre.Rcheck/tigre-Ex.timings

nameusersystemelapsed
ExpressionTimeSeries-class0.0040.0010.005
GPLearn1.1440.0971.291
GPModel-class0.0010.0010.002
GPPlot0.0020.0000.002
GPRankTargets0.0020.0000.001
SCGoptim0.0000.0000.001
expTransform0.0010.0000.001
export0.0020.0000.003
generateModels0.0020.0000.001
gpsimCreate0.0010.0000.001
kernCompute0.0020.0000.001
kernCreate0.0090.0000.009
kernDiagGradX0.0020.0010.003
kernGradient0.0020.0000.002
lnDiffErfs0.0010.0000.001
modelDisplay0.1400.0110.151
modelExpandParam0.0020.0000.001
modelExtractParam0.1030.0080.113
modelGradient0.1490.0070.160
modelTieParam0.0080.0000.008
optimiDefaultConstraint0.0020.0010.002
plotTimeseries0.1500.0060.161
processData6.3350.2367.489
scoreList-class0.0040.0010.005
tigre-package0.0030.0010.003