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BioC 3.3: CHECK report for FEM on moscato2

This page was generated on 2016-10-13 12:53:11 -0700 (Thu, 13 Oct 2016).

Package 380/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FEM 2.8.0
Andrew E. Teschendorff
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/FEM
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: FEM
Version: 2.8.0
Command: rm -rf FEM.buildbin-libdir FEM.Rcheck && mkdir FEM.buildbin-libdir FEM.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FEM.buildbin-libdir FEM_2.8.0.tar.gz >FEM.Rcheck\00install.out 2>&1 && cp FEM.Rcheck\00install.out FEM-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=FEM.buildbin-libdir --install="check:FEM-install.out" --force-multiarch --no-vignettes --timings FEM_2.8.0.tar.gz
StartedAt: 2016-10-13 03:41:47 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 03:48:58 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 431.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: FEM.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf FEM.buildbin-libdir FEM.Rcheck && mkdir FEM.buildbin-libdir FEM.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FEM.buildbin-libdir FEM_2.8.0.tar.gz >FEM.Rcheck\00install.out 2>&1 && cp FEM.Rcheck\00install.out FEM-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=FEM.buildbin-libdir --install="check:FEM-install.out" --force-multiarch --no-vignettes --timings FEM_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/FEM.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FEM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FEM' version '2.8.0'
* 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 whether package 'FEM' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'igraph::intersection' by 'graph::intersection' when loading 'FEM'
  Warning: replacing previous import 'igraph::union' by 'graph::union' when loading 'FEM'
  Warning: replacing previous import 'igraph::degree' by 'graph::degree' when loading 'FEM'
  Warning: replacing previous import 'igraph::edges' by 'graph::edges' when loading 'FEM'
  Warning: replacing previous import 'limma::plotMA' by 'BiocGenerics::plotMA' when loading 'FEM'
  Warning: replacing previous import 'igraph::normalize' by 'BiocGenerics::normalize' when loading 'FEM'
See 'E:/biocbld/bbs-3.3-bioc/meat/FEM.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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 ... 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 'var'
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 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 symbols var
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "symbols")
  importFrom("stats", "model.matrix", "var")
  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:30-32: Dropping empty section \details
prepare_Rd: DoIntEpi450k.Rd:47-49: Dropping empty section \note
prepare_Rd: DoIntEpi450k.Rd:53-55: Dropping empty section \seealso
prepare_Rd: DoIntEpi450k.Rd:56-58: 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:41-43: Dropping empty section \details
prepare_Rd: DoIntFEM450k.Rd:60-62: Dropping empty section \note
prepare_Rd: DoIntFEM450k.Rd:66-68: Dropping empty section \seealso
prepare_Rd: DoIntFEM450k.Rd:69-71: 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:25-27: Dropping empty section \details
prepare_Rd: GenStatM.Rd:43-45: Dropping empty section \note
prepare_Rd: GenStatM.Rd:49-51: Dropping empty section \seealso
prepare_Rd: GenStatM.Rd:52-54: 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
* 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 installed files from '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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
FemModShow 15.93   0.93   16.86
DoExpMod   14.75   0.03   14.79
DoFEMbi    14.34   0.02   14.35
DoEpiMod   13.34   0.05   13.73
Toydata    12.27   0.24   12.51
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
DoFEMbi    17.03   0.03   17.06
DoEpiMod   16.21   0.07   16.46
Toydata    15.94   0.21   16.15
DoExpMod   15.68   0.00   15.68
FemModShow 11.67   0.51   12.19
* 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 WARNINGs, 5 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/FEM.Rcheck/00check.log'
for details.

FEM.Rcheck/00install.out:


install for i386

* installing *source* package 'FEM' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'igraph::intersection' by 'graph::intersection' when loading 'FEM'
Warning: replacing previous import 'igraph::union' by 'graph::union' when loading 'FEM'
Warning: replacing previous import 'igraph::degree' by 'graph::degree' when loading 'FEM'
Warning: replacing previous import 'igraph::edges' by 'graph::edges' when loading 'FEM'
Warning: replacing previous import 'limma::plotMA' by 'BiocGenerics::plotMA' when loading 'FEM'
Warning: replacing previous import 'igraph::normalize' by 'BiocGenerics::normalize' when loading 'FEM'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'igraph::intersection' by 'graph::intersection' when loading 'FEM'
Warning: replacing previous import 'igraph::union' by 'graph::union' when loading 'FEM'
Warning: replacing previous import 'igraph::degree' by 'graph::degree' when loading 'FEM'
Warning: replacing previous import 'igraph::edges' by 'graph::edges' when loading 'FEM'
Warning: replacing previous import 'limma::plotMA' by 'BiocGenerics::plotMA' when loading 'FEM'
Warning: replacing previous import 'igraph::normalize' by 'BiocGenerics::normalize' when loading 'FEM'

install for x64

* installing *source* package 'FEM' ...
** 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::normalize' by 'BiocGenerics::normalize' when loading 'FEM'
* MD5 sums
packaged installation of 'FEM' as FEM_2.8.0.zip
* DONE (FEM)

FEM.Rcheck/examples_i386/FEM-Ex.timings:

nameusersystemelapsed
DoEpiMod13.34 0.0513.73
DoExpMod14.75 0.0314.79
DoFEMbi14.34 0.0214.35
FemModShow15.93 0.9316.86
Realdata000
Toydata12.27 0.2412.51

FEM.Rcheck/examples_x64/FEM-Ex.timings:

nameusersystemelapsed
DoEpiMod16.21 0.0716.46
DoExpMod15.68 0.0015.68
DoFEMbi17.03 0.0317.06
FemModShow11.67 0.5112.19
Realdata000
Toydata15.94 0.2116.15