Oliver Philipp
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/Path2PPI |
| Branch: RELEASE_3_12 |
| Last Commit: 57601d8 |
| Last Changed Date: 2020-10-27 11:07:31 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:41 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the Path2PPI package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1302/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Path2PPI 1.20.0 (landing page) Oliver Philipp
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Path2PPI |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Path2PPI.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Path2PPI_1.20.0.tar.gz |
| StartedAt: 2021-05-06 05:22:52 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:24:30 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 97.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Path2PPI.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Path2PPI.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Path2PPI_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/Path2PPI.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.20.0'
* 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 5.36 0 5.36
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
predictPPI 6.3 0 6.32
* 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-3.12-bioc/meat/Path2PPI.Rcheck/00check.log'
for details.
Path2PPI.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/Path2PPI_1.20.0.tar.gz && rm -rf Path2PPI.buildbin-libdir && mkdir Path2PPI.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Path2PPI.buildbin-libdir Path2PPI_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Path2PPI_1.20.0.zip && rm Path2PPI_1.20.0.tar.gz Path2PPI_1.20.0.zip
###
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% 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 617k 0 2677 0 0 83250 0 0:00:07 --:--:-- 0:00:07 83656
100 617k 100 617k 0 0 15.5M 0 --:--:-- --:--:-- --:--:-- 15.4M
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_1.20.0.zip
* DONE (Path2PPI)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'Path2PPI' successfully unpacked and MD5 sums checked
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Path2PPI.Rcheck/tests_i386/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 -- Thu May 06 05:24:21 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
4.95 0.15 5.07
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Path2PPI.Rcheck/tests_x64/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 -- Thu May 06 05:24:25 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
3.09 0.07 3.15
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Path2PPI.Rcheck/examples_i386/Path2PPI-Ex.timings
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Path2PPI.Rcheck/examples_x64/Path2PPI-Ex.timings
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