Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:15 -0400 (Fri, 15 Oct 2021).

CHECK results for Path2PPI on tokay2

To the developers/maintainers of the Path2PPI package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Path2PPI.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1347/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Path2PPI 1.22.0  (landing page)
Oliver Philipp
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/Path2PPI
git_branch: RELEASE_3_13
git_last_commit: 0ce380a
git_last_commit_date: 2021-05-19 12:15:15 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Path2PPI
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Path2PPI.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Path2PPI_1.22.0.tar.gz
StartedAt: 2021-10-15 03:10:41 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 03:12:28 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 106.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Path2PPI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Path2PPI.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Path2PPI_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Path2PPI.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Path2PPI/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Path2PPI' version '1.22.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
  '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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
predictPPI 5.02      0    5.01
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
predictPPI 5.63      0    5.62
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/Path2PPI.Rcheck/00check.log'
for details.



Installation output

Path2PPI.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Path2PPI_1.22.0.tar.gz && rm -rf Path2PPI.buildbin-libdir && mkdir Path2PPI.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Path2PPI.buildbin-libdir Path2PPI_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Path2PPI_1.22.0.zip && rm Path2PPI_1.22.0.tar.gz Path2PPI_1.22.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0  615k    0  5187    0     0  63393      0  0:00:09 --:--:--  0:00:09 63256
100  615k  100  615k    0     0  2003k      0 --:--:-- --:--:-- --:--:-- 2005k

install for i386

* installing *source* package 'Path2PPI' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Path2PPI'
    finding HTML links ... done
    Path2PPI                                html  
    addReference                            html  
    ai                                      html  
    getHybridNetwork                        html  
    getPPI                                  html  
    homologyScore                           html  
    plot.Path2PPI                           html  
    finding level-2 HTML links ... done

    predictPPI                              html  
    removeReference                         html  
    showInteraction                         html  
    showReferences                          html  
** 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

install for x64

* installing *source* package 'Path2PPI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Path2PPI' as Path2PPI_1.22.0.zip
* DONE (Path2PPI)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'Path2PPI' successfully unpacked and MD5 sums checked

Tests output

Path2PPI.Rcheck/tests_i386/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 -- Fri Oct 15 03:12:07 2021 
*********************************************** 
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 
   3.28    0.15    3.42 

Path2PPI.Rcheck/tests_x64/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Fri Oct 15 03:12:11 2021 
*********************************************** 
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 
   3.20    0.14    3.31 

Example timings

Path2PPI.Rcheck/examples_i386/Path2PPI-Ex.timings

nameusersystemelapsed
Path2PPI000
addReference0.770.000.77
ai0.180.000.17
getHybridNetwork1.950.011.97
getPPI2.320.002.31
homologyScore000
plot.Path2PPI2.290.042.33
predictPPI5.020.005.01
removeReference0.510.010.54
showInteraction2.210.002.20
showReferences0.560.020.58

Path2PPI.Rcheck/examples_x64/Path2PPI-Ex.timings

nameusersystemelapsed
Path2PPI000
addReference1.220.061.28
ai0.280.010.30
getHybridNetwork2.910.022.92
getPPI3.070.003.08
homologyScore000
plot.Path2PPI303
predictPPI5.630.005.62
removeReference0.510.000.52
showInteraction2.220.032.25
showReferences0.530.000.53