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BioC 3.5: CHECK report for Path2PPI on toluca2

This page was generated on 2017-04-23 14:40:26 -0400 (Sun, 23 Apr 2017).

Package 945/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Path2PPI 1.5.0
Oliver Philipp
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Path2PPI
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Path2PPI
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Path2PPI_1.5.0.tar.gz
StartedAt: 2017-04-23 07:43:43 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 07:44:43 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 59.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Path2PPI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Path2PPI_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Path2PPI.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Path2PPI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Path2PPI’ version ‘1.5.0’
* 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 ‘Path2PPI’ 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 ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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
.getInteractions,.ReferenceSpecies: no visible global function
  definition for ‘combn’
addReference,Path2PPI: no visible global function definition for
  ‘read.table’
initialize,.ReferenceSpecies: no visible global function definition for
  ‘read.table’
plot.Path2PPI,Path2PPI: no visible global function definition for ‘rgb’
plot.Path2PPI,Path2PPI: no visible global function definition for
  ‘rainbow’
plot.Path2PPI,Path2PPI: no visible global function definition for ‘par’
plot.Path2PPI,Path2PPI: no visible global function definition for
  ‘adjustcolor’
plot.Path2PPI,Path2PPI: no visible global function definition for
  ‘plot’
plot.Path2PPI,Path2PPI: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  adjustcolor combn legend par plot rainbow read.table rgb
Consider adding
  importFrom("grDevices", "adjustcolor", "rainbow", "rgb")
  importFrom("graphics", "legend", "par", "plot")
  importFrom("utils", "combn", "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
predictPPI 9.258  0.039   9.304
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Path2PPI.Rcheck/00check.log’
for details.


Path2PPI.Rcheck/00install.out:

* installing *source* package ‘Path2PPI’ ...
** 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 (Path2PPI)

Path2PPI.Rcheck/Path2PPI-Ex.timings:

nameusersystemelapsed
Path2PPI0.0010.0000.001
addReference1.0370.0421.080
ai0.2070.0100.217
getHybridNetwork3.7020.0343.740
getPPI3.9420.0393.987
homologyScore0.0010.0000.001
plot.Path2PPI4.6240.0304.662
predictPPI9.2580.0399.304
removeReference0.7170.0180.736
showInteraction3.6190.0233.645
showReferences0.7560.0270.783