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CHECK report for FEM on merida2

This page was generated on 2018-10-17 08:53:42 -0400 (Wed, 17 Oct 2018).

Package 485/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FEM 3.8.0
Zhen Yang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/FEM
Branch: RELEASE_3_7
Last Commit: a509b83
Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: FEM
Version: 3.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FEM_3.8.0.tar.gz
StartedAt: 2018-10-16 21:20:32 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:23:47 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 194.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: FEM.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FEM_3.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/FEM.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FEM’ version ‘3.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘AnnotationDbi’ ‘Matrix’ ‘marray’ ‘corrplot’ ‘igraph’ ‘impute’
  ‘limma’ ‘org.Hs.eg.db’ ‘graph’ ‘BiocGenerics’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘FEM’ can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
  Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’
  Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’
  Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’
  Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’
  Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’
  Warning: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’
  Warning: replacing previous import ‘Matrix::colSums’ by ‘BiocGenerics::colSums’ when loading ‘FEM’
  Warning: replacing previous import ‘Matrix::colMeans’ by ‘BiocGenerics::colMeans’ when loading ‘FEM’
  Warning: replacing previous import ‘Matrix::rowMeans’ by ‘BiocGenerics::rowMeans’ when loading ‘FEM’
  Warning: replacing previous import ‘Matrix::rowSums’ by ‘BiocGenerics::rowSums’ when loading ‘FEM’
  Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’
  Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’
See ‘/Users/biocbuild/bbs-3.7-bioc/meat/FEM.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... NOTE
  installed size is 13.6Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graph’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
* 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
DoEpiMod: no visible global function definition for ‘mappedkeys’
DoEpiMod: no visible global function definition for ‘write.table’
DoExpMod: no visible global function definition for ‘mappedkeys’
DoExpMod: no visible global function definition for ‘write.table’
DoFEMbi: no visible global function definition for ‘mappedkeys’
DoFEMbi: no visible global function definition for ‘write.table’
FemModShow : mycircle : <anonymous>: no visible global function
  definition for ‘symbols’
FemModShow: no visible global function definition for ‘pdf’
FemModShow: no visible global function definition for ‘dev.off’
GenStatM: no visible global function definition for ‘data’
GenStatM: no visible binding for global variable ‘probe450kfemanno’
GenStatM: no visible binding for global variable ‘probeEPICfemanno’
GenStatM: no visible global function definition for ‘model.matrix’
GenStatMsp: no visible global function definition for ‘data’
GenStatMsp: no visible binding for global variable ‘probe450kfemanno’
GenStatMsp: no visible binding for global variable ‘probeEPICfemanno’
GenStatMsp: no visible global function definition for ‘model.matrix’
GenStatR: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  data dev.off mappedkeys model.matrix pdf probe450kfemanno
  probeEPICfemanno symbols write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "symbols")
  importFrom("stats", "model.matrix")
  importFrom("utils", "data", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: DoEpiMod.Rd:44-46: Dropping empty section \details
prepare_Rd: DoEpiMod.Rd:71-73: Dropping empty section \note
prepare_Rd: DoEpiMod.Rd:77-79: Dropping empty section \seealso
prepare_Rd: DoExpMod.Rd:93: Dropping empty section \keyword
prepare_Rd: DoExpMod.Rd:94: Dropping empty section \keyword
prepare_Rd: DoExpMod.Rd:46-48: Dropping empty section \details
prepare_Rd: DoExpMod.Rd:72-74: Dropping empty section \note
prepare_Rd: DoExpMod.Rd:78-80: Dropping empty section \seealso
prepare_Rd: DoFEMbi.Rd:45-47: Dropping empty section \details
prepare_Rd: DoFEMbi.Rd:71-73: Dropping empty section \note
prepare_Rd: DoFEMbi.Rd:77-79: Dropping empty section \seealso
prepare_Rd: DoIntEpi450k.Rd:34-36: Dropping empty section \details
prepare_Rd: DoIntEpi450k.Rd:52-54: Dropping empty section \note
prepare_Rd: DoIntEpi450k.Rd:58-60: Dropping empty section \seealso
prepare_Rd: DoIntEpi450k.Rd:61-63: Dropping empty section \examples
prepare_Rd: DoIntExp.Rd:29-31: Dropping empty section \details
prepare_Rd: DoIntExp.Rd:47-49: Dropping empty section \note
prepare_Rd: DoIntExp.Rd:53-55: Dropping empty section \seealso
prepare_Rd: DoIntExp.Rd:56-57: Dropping empty section \examples
prepare_Rd: DoIntFEM450k.Rd:45-47: Dropping empty section \details
prepare_Rd: DoIntFEM450k.Rd:64-66: Dropping empty section \note
prepare_Rd: DoIntFEM450k.Rd:70-72: Dropping empty section \seealso
prepare_Rd: DoIntFEM450k.Rd:73-75: Dropping empty section \examples
prepare_Rd: FEM-package.Rd:47-48: Dropping empty section \seealso
prepare_Rd: FEM-package.Rd:49-51: Dropping empty section \examples
prepare_Rd: FemModShow.Rd:33-35: Dropping empty section \details
prepare_Rd: FemModShow.Rd:47-49: Dropping empty section \note
prepare_Rd: FemModShow.Rd:53-55: Dropping empty section \seealso
prepare_Rd: GenStatM.Rd:29-31: Dropping empty section \details
prepare_Rd: GenStatM.Rd:47-49: Dropping empty section \note
prepare_Rd: GenStatM.Rd:53-55: Dropping empty section \seealso
prepare_Rd: GenStatM.Rd:56-58: Dropping empty section \examples
prepare_Rd: GenStatMsp.Rd:32-34: Dropping empty section \details
prepare_Rd: GenStatMsp.Rd:51-53: Dropping empty section \note
prepare_Rd: GenStatMsp.Rd:57-59: Dropping empty section \seealso
prepare_Rd: GenStatMsp.Rd:60-62: Dropping empty section \examples
prepare_Rd: GenStatR.Rd:26-28: Dropping empty section \details
prepare_Rd: GenStatR.Rd:43-45: Dropping empty section \note
prepare_Rd: GenStatR.Rd:49-51: Dropping empty section \seealso
prepare_Rd: GenStatR.Rd:52-54: Dropping empty section \examples
prepare_Rd: Realdata.Rd:28-29: Dropping empty section \format
prepare_Rd: Realdata.Rd:30-32: Dropping empty section \details
prepare_Rd: Realdata.Rd:33-35: Dropping empty section \source
prepare_Rd: Toydata.Rd:27-29: Dropping empty section \details
prepare_Rd: Toydata.Rd:30-32: Dropping empty section \source
prepare_Rd: probe450kfemanno.Rd:27-28: Dropping empty section \format
prepare_Rd: probe450kfemanno.Rd:29-30: Dropping empty section \details
prepare_Rd: probe450kfemanno.Rd:31-33: Dropping empty section \source
prepare_Rd: probe450kfemanno.Rd:40-41: Dropping empty section \examples
prepare_Rd: probeEPICfemanno.Rd:27-28: Dropping empty section \format
prepare_Rd: probeEPICfemanno.Rd:29-30: Dropping empty section \details
prepare_Rd: probeEPICfemanno.Rd:31-33: Dropping empty section \source
prepare_Rd: probeEPICfemanno.Rd:40-41: Dropping empty section \examples
* 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 ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files contain a license that requires
distribution of original sources:
  ‘xcolor.sty’
Please ensure that you have complied with it.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
FemModShow 12.912  1.228  14.191
Toydata     7.868  0.359   8.267
DoFEMbi     7.997  0.142   8.202
DoEpiMod    7.598  0.211   7.855
DoExpMod    7.284  0.072   7.396
* 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 WARNINGs, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/FEM.Rcheck/00check.log’
for details.



Installation output

FEM.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘FEM’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’
Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colSums’ by ‘BiocGenerics::colSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colMeans’ by ‘BiocGenerics::colMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowMeans’ by ‘BiocGenerics::rowMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowSums’ by ‘BiocGenerics::rowSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’
Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colSums’ by ‘BiocGenerics::colSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colMeans’ by ‘BiocGenerics::colMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowMeans’ by ‘BiocGenerics::rowMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowSums’ by ‘BiocGenerics::rowSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’
* DONE (FEM)

Tests output

FEM.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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("FEM")

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, lengths, 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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

corrplot 0.84 loaded

Attaching package: 'igraph'

The following object is masked from 'package:IRanges':

    union

The following object is masked from 'package:S4Vectors':

    union

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

    normalize, path, union

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

    decompose, spectrum

The following object is masked from 'package:base':

    union



Attaching package: 'graph'

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

    degree, edges, intersection

[1] ".setUp"
[1] "Constructing weighted network"
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[1] "Running Spin-Glass algorithm"
[1] "Done for seed 1"
[1] "Module Sizes="
166929 
    36 
[1] "Modularity values="
  166929 
4.170086 
[1] "Starting Monte Carlo Runs"
[1] "Done for seed/module 1"
166929 
     0 
[1] "Summarising and generating output"
[1] 1
[1] "166929"


RUNIT TEST PROTOCOL -- Tue Oct 16 21:23:41 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
FEM RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
There were 13 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 12.451   0.491  12.965 

Example timings

FEM.Rcheck/FEM-Ex.timings

nameusersystemelapsed
DoEpiMod7.5980.2117.855
DoExpMod7.2840.0727.396
DoFEMbi7.9970.1428.202
FemModShow12.912 1.22814.191
Realdata0.0010.0000.001
Toydata7.8680.3598.267