Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).

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? here 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 344/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORfeeder 1.32.0  (landing page)
E.Gjerga
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/CNORfeeder
git_branch: RELEASE_3_13
git_last_commit: 297743c
git_last_commit_date: 2021-05-19 11:58:14 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.32.0
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_1.32.0.tar.gz
StartedAt: 2021-10-14 17:34:51 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 17:36:38 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 107.0 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_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CNORfeeder.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.32.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-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/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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: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, 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-2.2.6.1 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 -- Thu Oct 14 17:36:27 2021 
*********************************************** 
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 
  4.431   0.287   4.698

Example timings

CNORfeeder.Rcheck/CNORfeeder-Ex.timings

nameusersystemelapsed
Binference1.4830.0810.932
CNORfeeder-package0.7660.0170.785
MIinference0.4120.0050.418
buildFeederObjectDynamic1.6200.0511.672
gaBinaryT1W0.7810.0770.860
identifyMisfitIndices0.0360.0030.038
integrateLinks0.0320.0050.036
linksRanking0.0650.0010.066
makeBTables0.0310.0010.032
mapBTables2model0.6820.0150.697
mapDDN2model0.0550.0030.058
runDynamicFeeder0.0050.0020.007
weighting0.7190.0140.734