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BioC 3.5: CHECK report for GRridge on malbec2

This page was generated on 2017-08-16 13:18:04 -0400 (Wed, 16 Aug 2017).

Package 597/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRridge 1.0.0
Mark A. van de Wiel
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/GRridge
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GRridge
Version: 1.0.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GRridge_1.0.0.tar.gz
StartedAt: 2017-08-15 23:40:30 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:48:10 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 460.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GRridge.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GRridge_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GRridge.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRridge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRridge’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘penalized’ ‘Iso’ ‘survival’ ‘GSEABase’ ‘BiocGenerics’ ‘Biobase’
  ‘annotate’ ‘graph’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GRridge’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘stats::xtabs’ by ‘BiocGenerics::xtabs’ when loading ‘GRridge’
  Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘GRridge’
  Warning: replacing previous import ‘stats::mad’ by ‘BiocGenerics::mad’ when loading ‘GRridge’
  Warning: replacing previous import ‘stats::IQR’ by ‘BiocGenerics::IQR’ when loading ‘GRridge’
  Warning: replacing previous import ‘GSEABase::intersect’ by ‘BiocGenerics::intersect’ when loading ‘GRridge’
  Warning: replacing previous import ‘penalized::as.data.frame’ by ‘BiocGenerics::as.data.frame’ when loading ‘GRridge’
  Warning: replacing previous import ‘GSEABase::setdiff’ by ‘BiocGenerics::setdiff’ when loading ‘GRridge’
  Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘GRridge’
See ‘/home/biocbuild/bbs-3.5-bioc/meat/GRridge.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                    old_size new_size compress
  dataFarkas.rda       3.4Mb    2.5Mb    bzip2
  dataWurdinger.rda    1.9Mb    1.2Mb       xz
* 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
predict.grridge 196.760  0.808 206.607
grridgeCV        84.716  0.668  85.441
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/GRridge.Rcheck/00check.log’
for details.


GRridge.Rcheck/00install.out:

* installing *source* package ‘GRridge’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘stats::xtabs’ by ‘BiocGenerics::xtabs’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::mad’ by ‘BiocGenerics::mad’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::IQR’ by ‘BiocGenerics::IQR’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::intersect’ by ‘BiocGenerics::intersect’ when loading ‘GRridge’
Warning: replacing previous import ‘penalized::as.data.frame’ by ‘BiocGenerics::as.data.frame’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::setdiff’ by ‘BiocGenerics::setdiff’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘GRridge’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘stats::xtabs’ by ‘BiocGenerics::xtabs’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::mad’ by ‘BiocGenerics::mad’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::IQR’ by ‘BiocGenerics::IQR’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::intersect’ by ‘BiocGenerics::intersect’ when loading ‘GRridge’
Warning: replacing previous import ‘penalized::as.data.frame’ by ‘BiocGenerics::as.data.frame’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::setdiff’ by ‘BiocGenerics::setdiff’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘GRridge’
* DONE (GRridge)

GRridge.Rcheck/GRridge-Ex.timings:

nameusersystemelapsed
CreatePartition0.0680.0040.070
PartitionsSelection0.0000.0000.002
auc0.3760.0120.385
dataFarkas0.3560.0000.357
dataVerlaat0.040.000.04
dataWurdinger2.2960.0442.343
grridge0.1000.0040.103
grridgeCV84.716 0.66885.441
hello000
matchGeneSets1.2680.0001.267
mergeGroups1.7960.0041.803
predict.grridge196.760 0.808206.607
roc1.9240.0081.933