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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Path2PPI.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings Path2PPI_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/Path2PPI.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘Path2PPI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Path2PPI’ version ‘1.28.0’
* 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
  ‘legend’
Undefined global functions or variables:
  adjustcolor combn legend par rainbow read.table rgb
Consider adding
  importFrom("grDevices", "adjustcolor", "rainbow", "rgb")
  importFrom("graphics", "legend", "par")
  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 (user + system) or elapsed time > 5s
                  user system elapsed
predictPPI      10.291  0.036  21.736
showInteraction  4.834  0.100   9.877
plot.Path2PPI    4.372  0.067  16.133
getPPI           3.812  0.023   8.267
* 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 ...
  ‘Path2PPI-tutorial.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/Path2PPI.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL Path2PPI
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘Path2PPI’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Path2PPI)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 -- Mon Apr 10 22:44:45 2023 
*********************************************** 
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 
  5.145   0.163   6.180