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BioC 3.4: CHECK report for SemDist on malbec1

This page was generated on 2017-04-15 16:12:18 -0400 (Sat, 15 Apr 2017).

Package 1121/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SemDist 1.8.0
Ian Gonzalez
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/SemDist
Last Changed Rev: 123129 / Revision: 128728
Last Changed Date: 2016-10-27 18:03:18 -0400 (Thu, 27 Oct 2016)
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: SemDist
Version: 1.8.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SemDist_1.8.0.tar.gz
StartedAt: 2017-04-15 01:11:32 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:12:50 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 77.2 seconds
RetCode: 0
Status:  OK 
CheckDir: SemDist.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SemDist_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SemDist.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SemDist/DESCRIPTION’ ... OK
* this is package ‘SemDist’ version ‘1.8.0’
* 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 ‘SemDist’ 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
RUMIcurve : IA_sum: no visible global function definition for ‘na.omit’
computeIA: no visible global function definition for ‘read.table’
findRUMI : IA_sum: no visible global function definition for ‘na.omit’
getPredictions: no visible global function definition for ‘read.table’
getTrues: no visible global function definition for ‘read.table’
loadIA: no visible global function definition for ‘data’
readOntology: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  data na.omit read.table
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data", "read.table")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
RUMIcurve 5.136  0.008   5.149
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/SemDist.Rcheck/00check.log’
for details.


SemDist.Rcheck/00install.out:

* installing *source* package ‘SemDist’ ...
** 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 (SemDist)

SemDist.Rcheck/SemDist-Ex.timings:

nameusersystemelapsed
IAccr0.0200.0000.021
RUMIcurve5.1360.0085.149
computeIA0.6320.0040.636
findRUMI0.9360.0000.934
parentcnt0.0040.0000.005
termcnt0.0040.0000.004