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CHECK report for CNORfeeder on merida2

This page was generated on 2019-04-09 13:28:02 -0400 (Tue, 09 Apr 2019).

Package 299/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORfeeder 1.23.1
F.Eduati
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CNORfeeder
Branch: master
Last Commit: e997b6d
Last Changed Date: 2019-01-04 13:25:41 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: CNORfeeder
Version: 1.23.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNORfeeder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNORfeeder_1.23.1.tar.gz
StartedAt: 2019-04-09 00:00:24 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:01:38 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 73.7 seconds
RetCode: 0
Status:  OK 
CheckDir: CNORfeeder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNORfeeder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNORfeeder_1.23.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CNORfeeder.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNORfeeder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORfeeder’ version ‘1.23.1’
* 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 ‘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
* 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
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’
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’
shift: no visible global function definition for ‘tail’
shift: no visible global function definition for ‘head’
Undefined global functions or variables:
  as head na.omit new 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/CNORfeeder.Rcheck/00check.log’
for details.

Installation output

CNORfeeder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNORfeeder
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CNORfeeder’ ...
** 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
* DONE (CNORfeeder)

Tests output

CNORfeeder.Rcheck/tests/runTests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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("CNORfeeder")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

hash-2.2.6.1 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  9 00:01:32 2019 
*********************************************** 
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 
  4.179   0.245   4.449

Example timings

CNORfeeder.Rcheck/CNORfeeder-Ex.timings

nameusersystemelapsed
Binference1.4010.0500.897
CNORfeeder-package0.7660.0310.804
MIinference0.3410.0030.351
gaBinaryT1W0.8180.0090.836
linksRanking0.050.000.05
makeBTables0.0320.0000.033
mapBTables2model0.7470.0090.771
mapDDN2model0.0520.0010.054
weighting0.7280.0070.743