Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:48 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

CHECK results for CNORfeeder on machv2


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.

raw results

Package 352/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORfeeder 1.34.0  (landing page)
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)
nebbiolo2Linux (Ubuntu 20.04.4 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: CNORfeeder
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNORfeeder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNORfeeder_1.34.0.tar.gz
StartedAt: 2022-04-12 11:44:01 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 11:46:04 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 122.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CNORfeeder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNORfeeder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNORfeeder_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CNORfeeder.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.34.0’
* 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 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 ... 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 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/CNORfeeder.Rcheck/00check.log’
for details.

Installation output

CNORfeeder.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CNORfeeder’ ...
** 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 (CNORfeeder)

Tests output

CNORfeeder.Rcheck/tests/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-apple-darwin17.0 (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: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 11:45:52 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 
  5.180   0.314   5.479

Example timings

CNORfeeder.Rcheck/CNORfeeder-Ex.timings

nameusersystemelapsed
Binference1.6130.0731.017
CNORfeeder-package0.8540.0210.875
MIinference0.3930.0050.397
buildFeederObjectDynamic1.9820.0712.054
gaBinaryT1W0.8600.0850.946
identifyMisfitIndices0.0300.0030.033
integrateLinks0.0300.0040.033
linksRanking0.0660.0010.067
makeBTables0.0330.0010.033
mapBTables2model0.6920.0160.708
mapDDN2model0.0550.0030.058
runDynamicFeeder0.0060.0030.008
weighting0.7410.0120.753