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BioC 3.1: CHECK report for tigre on zin2

This page was generated on 2015-10-09 09:24:00 -0700 (Fri, 09 Oct 2015).

Package 974/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tigre 1.22.0
Antti Honkela
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/tigre
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 ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.22.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings tigre_1.22.0.tar.gz
StartedAt: 2015-10-09 06:01:17 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 06:02:51 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 93.5 seconds
RetCode: 0
Status:  OK 
CheckDir: tigre.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings tigre_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/tigre.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tigre/DESCRIPTION’ ... OK
* this is package ‘tigre’ version ‘1.22.0’
* 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 ... [7s/7s] 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 ... NOTE
'library' or 'require' calls in package code:
  ‘lumi’ ‘puma’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
processData: no visible global function definition for ‘prcfive’
processData: no visible global function definition for ‘prctwfive’
processData: no visible global function definition for ‘prcfifty’
processData: no visible global function definition for ‘prcsevfive’
processData: no visible global function definition for ‘prcninfive’
processData: no visible global function definition for ‘se.exprs’
updateObject,scoreList: no visible global function definition for
  ‘getObjectSlots’
* 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 ... [7s/8s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/tigre.Rcheck/00check.log’
for details.


tigre.Rcheck/00install.out:

* installing *source* package ‘tigre’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c miscCFunctions.c -o miscCFunctions.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o tigre.so miscCFunctions.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/tigre.Rcheck/tigre/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (tigre)

tigre.Rcheck/tigre-Ex.timings:

nameusersystemelapsed
ExpressionTimeSeries-class0.0010.0000.001
GPLearn1.1680.0191.309
GPModel-class0.0010.0000.001
GPPlot0.0010.0000.001
GPRankTargets0.0010.0000.000
SCGoptim0.0000.0000.001
expTransform0.0010.0000.000
export0.0010.0000.001
generateModels0.0000.0000.001
gpsimCreate0.0010.0000.000
kernCompute0.0010.0000.001
kernCreate0.0050.0000.004
kernDiagGradX0.0010.0000.001
kernGradient0.0010.0000.002
lnDiffErfs0.0010.0000.000
modelDisplay0.1640.0000.165
modelExpandParam0.0010.0000.001
modelExtractParam0.1620.0000.161
modelGradient0.1950.0000.195
modelTieParam0.0030.0000.003
optimiDefaultConstraint0.0010.0000.001
plotTimeseries0.1690.0000.170
processData2.5490.0762.623
scoreList-class0.0010.0000.002
tigre-package0.0010.0000.001