Oliver Philipp
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/Path2PPI |
| Branch: master |
| Last Commit: bda44ef |
| Last Changed Date: 2019-10-29 13:39:49 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:43:06 -0500 (Thu, 16 Jan 2020).
| Package 1221/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Path2PPI 1.17.0 Oliver Philipp
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: Path2PPI |
| Version: 1.17.0 |
| 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_1.17.0.tar.gz |
| StartedAt: 2020-01-16 07:15:18 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 07:17:19 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 120.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Path2PPI.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Path2PPI.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.17.0’
* 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 (user + system) or elapsed time > 5s
user system elapsed
predictPPI 14.863 0.127 21.678
getPPI 5.711 0.129 5.842
getHybridNetwork 5.677 0.100 8.413
plot.Path2PPI 5.564 0.097 5.662
showInteraction 5.308 0.089 5.604
* 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-3.11-bioc/meat/Path2PPI.Rcheck/00check.log’
for details.
Path2PPI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Path2PPI ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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)
Path2PPI.Rcheck/tests/runTests.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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 -- Thu Jan 16 07:17:08 2020
***********************************************
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
7.039 0.346 10.770
Path2PPI.Rcheck/Path2PPI-Ex.timings
| name | user | system | elapsed | |
| Path2PPI | 0.002 | 0.001 | 0.002 | |
| addReference | 1.665 | 0.171 | 2.816 | |
| ai | 0.296 | 0.025 | 0.362 | |
| getHybridNetwork | 5.677 | 0.100 | 8.413 | |
| getPPI | 5.711 | 0.129 | 5.842 | |
| homologyScore | 0.001 | 0.001 | 0.001 | |
| plot.Path2PPI | 5.564 | 0.097 | 5.662 | |
| predictPPI | 14.863 | 0.127 | 21.678 | |
| removeReference | 0.824 | 0.042 | 0.866 | |
| showInteraction | 5.308 | 0.089 | 5.604 | |
| showReferences | 1.017 | 0.058 | 1.075 | |