E.Gjerga
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/CNORfeeder |
| git_branch: RELEASE_3_14 |
| git_last_commit: 39356db |
| git_last_commit_date: 2021-10-26 12:07:24 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:21 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the CNORfeeder package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNORfeeder.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 352/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNORfeeder 1.34.0 (landing page) E.Gjerga
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CNORfeeder |
| Version: 1.34.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNORfeeder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CNORfeeder_1.34.0.tar.gz |
| StartedAt: 2022-04-12 17:33:33 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 17:35:58 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 144.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNORfeeder.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNORfeeder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CNORfeeder_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CNORfeeder.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNORfeeder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNORfeeder' version '1.34.0'
* 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 'CNORfeeder' 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 ... OK
* 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 ... NOTE
'library' or 'require' call to 'MEIGOR' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Binference: no visible global function definition for 'write.table'
MIinference: no visible global function definition for 'as'
MIinference: no visible global function definition for 'write.table'
gaBinaryT1W: no visible global function definition for 'runif'
getLBodeContObjFunctionWeighted: no visible global function definition
for 'incidence2Adjacency'
getLBodeContObjFunctionWeighted: no visible global function definition
for 'getLBodeSimFunction'
integrateLinks: no visible global function definition for 'write.table'
linksRanking: no visible global function definition for 'write.table'
makeBTables: no visible global function definition for 'na.omit'
mapBTables2model: no visible global function definition for 'new'
parEstimationLBodeSSmWeighted: no visible global function definition
for 'incidence2Adjacency'
parEstimationLBodeSSmWeighted: no visible global function definition
for 'createLBodeContPars'
parEstimationLBodeSSmWeighted: no visible global function definition
for 'essR'
parEstimationLBodeWeighted: no visible global function definition for
'defaultParametersSSm'
parEstimationLBodeWeighted: no visible global function definition for
'defaultParametersGA'
parEstimationLBodeWeighted: no visible global function definition for
'parEstimationLBodeGA'
preprocessingWeighted: no visible global function definition for
'graph_from_graphnel'
preprocessingWeighted: no visible global function definition for
'get.adjacency'
preprocessingWeighted: no visible global function definition for
'all_simple_paths'
preprocessingWeighted: no visible global function definition for
'write.table'
runDynamicFeeder: no visible global function definition for
'defaultParametersSSm'
shift: no visible global function definition for 'tail'
shift: no visible global function definition for 'head'
Undefined global functions or variables:
all_simple_paths as createLBodeContPars defaultParametersGA
defaultParametersSSm essR get.adjacency getLBodeSimFunction
graph_from_graphnel head incidence2Adjacency na.omit new
parEstimationLBodeGA runif tail write.table
Consider adding
importFrom("methods", "as", "new")
importFrom("stats", "na.omit", "runif")
importFrom("utils", "head", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
Binference 0.15 0.02 16.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Binference 0.13 0 16.31
* 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-3.14-bioc/meat/CNORfeeder.Rcheck/00check.log'
for details.
CNORfeeder.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CNORfeeder_1.34.0.tar.gz && rm -rf CNORfeeder.buildbin-libdir && mkdir CNORfeeder.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNORfeeder.buildbin-libdir CNORfeeder_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CNORfeeder_1.34.0.zip && rm CNORfeeder_1.34.0.tar.gz CNORfeeder_1.34.0.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
20 3472k 20 717k 0 0 1477k 0 0:00:02 --:--:-- 0:00:02 1478k
100 3472k 100 3472k 0 0 2397k 0 0:00:01 0:00:01 --:--:-- 2399k
install for i386
* installing *source* package 'CNORfeeder' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CNORfeeder'
finding HTML links ... done
Binference html
finding level-2 HTML links ... done
CNORfeeder-package html
MIinference html
PPINigraph html
UniprotIDdream html
buildFeederObjectDynamic html
cnolist html
database html
feederObject html
gaBinaryT1W html
identifyMisfitIndices html
indices html
integrateLinks html
integratedModel html
linksRanking html
makeBTables html
mapBTables2model html
mapDDN2model html
model html
runDynamicFeeder html
simData html
weighting 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 'CNORfeeder' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNORfeeder' as CNORfeeder_1.34.0.zip
* DONE (CNORfeeder)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CNORfeeder' successfully unpacked and MD5 sums checked
|
CNORfeeder.Rcheck/tests_i386/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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("CNORfeeder")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
hash-2.2.6.2 provided by Decision Patterns
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
[1] "p38 : the condition with stimulus il1a and inhibitor p38 is missing or NA"
[1] "p38 : the condition with stimulus tgfa and inhibitor p38 is missing or NA"
[1] "mek12 : the condition with stimulus il1a and inhibitor mek12 is missing or NA"
[1] "mek12 : the condition with stimulus tgfa and inhibitor mek12 is missing or NA"
[1] "p38 : the condition with stimulus il1a and inhibitor p38 is missing or NA"
[1] "p38 : the condition with stimulus tgfa and inhibitor p38 is missing or NA"
[1] "mek12 : the condition with stimulus il1a and inhibitor mek12 is missing or NA"
[1] "mek12 : the condition with stimulus tgfa and inhibitor mek12 is missing or NA"
[1] "The following species are measured: akt, erk12, ikb, jnk12, p38, hsp27, mek12"
[1] "The following species are stimulated: igf1, il1a, tgfa, tnfa"
[1] "The following species are inhibited: ikk, mek12, pi3k, p38"
[1] "The following species are not observable and/or not controllable: "
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: akt"
[1] "Added links:"
[1] "igf1->akt"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: akt"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: akt"
[1] "Added links:"
[1] "tgfa->akt"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: akt"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: erk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: erk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: erk12"
[1] "Added links:"
[1] "tgfa->mek12"
[1] "!il1a+mek12->erk12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: erk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: ikb"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: ikb"
[1] "Added links:"
[1] "il1a->ikk"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: ikb"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: ikb"
[1] "Added links:"
[1] "tnfa->ikk"
[1] "jnk12->ikk"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: jnk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: jnk12"
[1] "Added links:"
[1] "il1a->jnk12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: jnk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: jnk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: p38"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: p38"
[1] "Added links:"
[1] "il1a->p38"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: p38"
[1] "Added links:"
[1] "ikk->p38"
[1] "ikb->p38"
[1] "mek12->p38"
[1] "erk12->p38"
[1] "hsp27->p38"
[1] "pi3k->p38"
[1] "akt->p38"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: p38"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: hsp27"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: hsp27"
[1] "Added links:"
[1] "il1a->p38"
[1] "!tgfa+p38->hsp27"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: hsp27"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: hsp27"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: mek12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: mek12"
[1] "Added links:"
[1] "il1a->mek12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: mek12"
[1] "Added links:"
[1] "tgfa->mek12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: mek12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "p38 : the condition with stimulus il1a and inhibitor p38 is missing or NA"
[1] "p38 : the condition with stimulus tgfa and inhibitor p38 is missing or NA"
[1] "mek12 : the condition with stimulus il1a and inhibitor mek12 is missing or NA"
[1] "mek12 : the condition with stimulus tgfa and inhibitor mek12 is missing or NA"
[1] "The following species are measured: akt, erk12, ikb, jnk12, p38, hsp27, mek12"
[1] "The following species are stimulated: igf1, il1a, tgfa, tnfa"
[1] "The following species are inhibited: ikk, mek12, pi3k, p38"
[1] "The following species are not observable and/or not controllable: "
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: akt"
[1] "Added links:"
[1] "igf1->akt"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: akt"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: akt"
[1] "Added links:"
[1] "tgfa->akt"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: akt"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: erk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: erk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: erk12"
[1] "Added links:"
[1] "tgfa->mek12"
[1] "!il1a+mek12->erk12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: erk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: ikb"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: ikb"
[1] "Added links:"
[1] "il1a->ikk"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: ikb"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: ikb"
[1] "Added links:"
[1] "tnfa->ikk"
[1] "jnk12->ikk"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: jnk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: jnk12"
[1] "Added links:"
[1] "il1a->jnk12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: jnk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: jnk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: p38"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: p38"
[1] "Added links:"
[1] "il1a->p38"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: p38"
[1] "Added links:"
[1] "ikk->p38"
[1] "ikb->p38"
[1] "mek12->p38"
[1] "erk12->p38"
[1] "hsp27->p38"
[1] "pi3k->p38"
[1] "akt->p38"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: p38"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: hsp27"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: hsp27"
[1] "Added links:"
[1] "il1a->p38"
[1] "!tgfa+p38->hsp27"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: hsp27"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: hsp27"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: mek12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: mek12"
[1] "Added links:"
[1] "il1a->mek12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: mek12"
[1] "Added links:"
[1] "tgfa->mek12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: mek12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
RUNIT TEST PROTOCOL -- Tue Apr 12 17:35:46 2022
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
CNORfeeder RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
3.43 0.15 3.56
|
CNORfeeder.Rcheck/tests_x64/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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("CNORfeeder")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
hash-2.2.6.2 provided by Decision Patterns
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
[1] "p38 : the condition with stimulus il1a and inhibitor p38 is missing or NA"
[1] "p38 : the condition with stimulus tgfa and inhibitor p38 is missing or NA"
[1] "mek12 : the condition with stimulus il1a and inhibitor mek12 is missing or NA"
[1] "mek12 : the condition with stimulus tgfa and inhibitor mek12 is missing or NA"
[1] "p38 : the condition with stimulus il1a and inhibitor p38 is missing or NA"
[1] "p38 : the condition with stimulus tgfa and inhibitor p38 is missing or NA"
[1] "mek12 : the condition with stimulus il1a and inhibitor mek12 is missing or NA"
[1] "mek12 : the condition with stimulus tgfa and inhibitor mek12 is missing or NA"
[1] "The following species are measured: akt, erk12, ikb, jnk12, p38, hsp27, mek12"
[1] "The following species are stimulated: igf1, il1a, tgfa, tnfa"
[1] "The following species are inhibited: ikk, mek12, pi3k, p38"
[1] "The following species are not observable and/or not controllable: "
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: akt"
[1] "Added links:"
[1] "igf1->akt"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: akt"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: akt"
[1] "Added links:"
[1] "tgfa->akt"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: akt"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: erk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: erk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: erk12"
[1] "Added links:"
[1] "tgfa->mek12"
[1] "!il1a+mek12->erk12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: erk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: ikb"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: ikb"
[1] "Added links:"
[1] "il1a->ikk"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: ikb"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: ikb"
[1] "Added links:"
[1] "tnfa->ikk"
[1] "jnk12->ikk"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: jnk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: jnk12"
[1] "Added links:"
[1] "il1a->jnk12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: jnk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: jnk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: p38"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: p38"
[1] "Added links:"
[1] "il1a->p38"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: p38"
[1] "Added links:"
[1] "ikk->p38"
[1] "ikb->p38"
[1] "mek12->p38"
[1] "erk12->p38"
[1] "hsp27->p38"
[1] "pi3k->p38"
[1] "akt->p38"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: p38"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: hsp27"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: hsp27"
[1] "Added links:"
[1] "il1a->p38"
[1] "!tgfa+p38->hsp27"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: hsp27"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: hsp27"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: mek12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: mek12"
[1] "Added links:"
[1] "il1a->mek12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: mek12"
[1] "Added links:"
[1] "tgfa->mek12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: mek12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "p38 : the condition with stimulus il1a and inhibitor p38 is missing or NA"
[1] "p38 : the condition with stimulus tgfa and inhibitor p38 is missing or NA"
[1] "mek12 : the condition with stimulus il1a and inhibitor mek12 is missing or NA"
[1] "mek12 : the condition with stimulus tgfa and inhibitor mek12 is missing or NA"
[1] "The following species are measured: akt, erk12, ikb, jnk12, p38, hsp27, mek12"
[1] "The following species are stimulated: igf1, il1a, tgfa, tnfa"
[1] "The following species are inhibited: ikk, mek12, pi3k, p38"
[1] "The following species are not observable and/or not controllable: "
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: akt"
[1] "Added links:"
[1] "igf1->akt"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: akt"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: akt"
[1] "Added links:"
[1] "tgfa->akt"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: akt"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: erk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: erk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: erk12"
[1] "Added links:"
[1] "tgfa->mek12"
[1] "!il1a+mek12->erk12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: erk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: ikb"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: ikb"
[1] "Added links:"
[1] "il1a->ikk"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: ikb"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: ikb"
[1] "Added links:"
[1] "tnfa->ikk"
[1] "jnk12->ikk"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: jnk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: jnk12"
[1] "Added links:"
[1] "il1a->jnk12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: jnk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: jnk12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: p38"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: p38"
[1] "Added links:"
[1] "il1a->p38"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: p38"
[1] "Added links:"
[1] "ikk->p38"
[1] "ikb->p38"
[1] "mek12->p38"
[1] "erk12->p38"
[1] "hsp27->p38"
[1] "pi3k->p38"
[1] "akt->p38"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: p38"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: hsp27"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: hsp27"
[1] "Added links:"
[1] "il1a->p38"
[1] "!tgfa+p38->hsp27"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: hsp27"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: hsp27"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: igf1 signal: mek12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: il1a signal: mek12"
[1] "Added links:"
[1] "il1a->mek12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tgfa signal: mek12"
[1] "Added links:"
[1] "tgfa->mek12"
[1] "---------------------------------------------"
[1] ""
[1] "---------------------------------------------"
[1] "stimulus: tnfa signal: mek12"
[1] "Added links:"
[1] "---------------------------------------------"
[1] ""
RUNIT TEST PROTOCOL -- Tue Apr 12 17:35:50 2022
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
CNORfeeder RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
3.32 0.14 3.45
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CNORfeeder.Rcheck/examples_i386/CNORfeeder-Ex.timings
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CNORfeeder.Rcheck/examples_x64/CNORfeeder-Ex.timings
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