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BioC 3.4: CHECK report for tigre on morelia

This page was generated on 2017-04-15 16:23:14 -0400 (Sat, 15 Apr 2017).

Package 1234/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tigre 1.28.1
Antti Honkela
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/tigre
Last Changed Rev: 127452 / Revision: 128728
Last Changed Date: 2017-03-15 22:03:50 -0400 (Wed, 15 Mar 2017)
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: tigre
Version: 1.28.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tigre_1.28.1.tar.gz
StartedAt: 2017-04-15 08:51:17 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 08:53:48 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 150.8 seconds
RetCode: 0
Status:  OK 
CheckDir: tigre.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tigre_1.28.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/tigre.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 ‘tigre/DESCRIPTION’ ... OK
* this is package ‘tigre’ version ‘1.28.1’
* 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 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 ... NOTE
GPPlot: no visible global function definition for ‘polygon’
export.scores: no visible global function definition for ‘png’
export.scores: no visible global function definition for ‘dev.off’
gpdisimLogLikeGradients: no visible global function definition for
  ‘tail’
[,scoreList: no visible global function definition for ‘slotNames’
c,scoreList: no visible global function definition for ‘slotNames’
Undefined global functions or variables:
  dev.off png polygon slotNames tail
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "polygon")
  importFrom("methods", "slotNames")
  importFrom("utils", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
processData 5.251  0.153   5.727
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/tigre.Rcheck/00check.log’
for details.


tigre.Rcheck/00install.out:

* installing *source* package ‘tigre’ ...
** 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 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 /Users/biocbuild/bbs-3.4-bioc/meat/tigre.Rcheck/tigre/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (tigre)

tigre.Rcheck/tigre-Ex.timings:

nameusersystemelapsed
ExpressionTimeSeries-class0.0020.0000.002
GPLearn1.5630.0742.526
GPModel-class0.0010.0000.001
GPPlot0.0000.0010.001
GPRankTargets0.0010.0000.001
SCGoptim0.0000.0000.001
expTransform0.0010.0000.001
export0.0020.0010.002
generateModels0.0010.0000.002
gpsimCreate0.0000.0000.001
kernCompute0.0020.0000.002
kernCreate0.0050.0000.006
kernDiagGradX0.0020.0000.002
kernGradient0.0020.0000.002
lnDiffErfs0.0010.0000.001
modelDisplay0.1530.0050.157
modelExpandParam0.0010.0000.001
modelExtractParam0.1500.0050.154
modelGradient0.1910.0030.194
modelTieParam0.0030.0000.004
optimiDefaultConstraint0.0010.0000.001
plotTimeseries0.1440.0050.149
processData5.2510.1535.727
scoreList-class0.0020.0010.003
tigre-package0.0010.0000.001