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CHECK report for Path2PPI on merida1

This page was generated on 2019-04-16 11:58:55 -0400 (Tue, 16 Apr 2019).

Package 1120/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Path2PPI 1.12.0
Oliver Philipp
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/Path2PPI
Branch: RELEASE_3_8
Last Commit: 1099cfc
Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Path2PPI
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Path2PPI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Path2PPI_1.12.0.tar.gz
StartedAt: 2019-04-16 01:46:23 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:48:00 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 97.3 seconds
RetCode: 0
Status:  OK 
CheckDir: Path2PPI.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Path2PPI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Path2PPI_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Path2PPI.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
predictPPI       14.680  0.065  20.305
getHybridNetwork  6.012  0.058   6.927
plot.Path2PPI     5.914  0.047   6.222
showInteraction   5.718  0.037   8.079
getPPI            5.199  0.057   5.296
* 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-3.8-bioc/meat/Path2PPI.Rcheck/00check.log’
for details.



Installation output

Path2PPI.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Path2PPI
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Path2PPI’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Path2PPI)

Tests output

Path2PPI.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("Path2PPI")

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
Begin with Homo sapiens
6 interactions processed. These lead to 0 interactions in target species.
-------------------------------
Begin with Saccharomyces cerevisiae (S288c)
15 interactions processed. These lead to 8 interactions in target species.
-------------------------------
Combine results to one single PPI.
A total of 8 putative interactions were predicted in target species.


RUNIT TEST PROTOCOL -- Tue Apr 16 01:47:53 2019 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Path2PPI RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  5.799   0.153   5.978 

Example timings

Path2PPI.Rcheck/Path2PPI-Ex.timings

nameusersystemelapsed
Path2PPI0.0020.0010.002
addReference2.7670.0784.781
ai0.2930.0180.396
getHybridNetwork6.0120.0586.927
getPPI5.1990.0575.296
homologyScore0.0000.0000.001
plot.Path2PPI5.9140.0476.222
predictPPI14.680 0.06520.305
removeReference1.8090.0261.855
showInteraction5.7180.0378.079
showReferences2.4280.0313.939