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BioC 3.0: CHECK report for FEM on perceval

This page was generated on 2015-04-10 10:00:29 -0700 (Fri, 10 Apr 2015).

Package 293/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FEM 1.0.0
Andrew E. Teschendorff , Yinming Jiao
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/FEM
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: FEM
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch FEM_1.0.0.tar.gz
StartedAt: 2015-04-10 01:19:41 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:25:56 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 375.1 seconds
RetCode: 0
Status:  OK 
CheckDir: FEM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch FEM_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/FEM.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Matrix’ ‘igraph’ ‘marray’ ‘corrplot’ ‘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 ... NOTE
Found the following hidden files and directories:
  vignettes/.IntroDoFEM.Rnw.swm
  vignettes/.IntroDoFEM.Rnw.swn
  vignettes/.IntroDoFEM.Rnw.swo
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 ‘FEM’ can be installed ... [27s/27s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘igraph’ ‘limma’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘BiocGenerics’ ‘graph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 binding for global variable ‘Entrez.GeneSybo.list’
DoEpiMod: no visible binding for global variable ‘toydata’
DoExpMod: no visible binding for global variable ‘Entrez.GeneSybo.list’
DoExpMod: no visible binding for global variable ‘toydata’
DoFEMbi: no visible binding for global variable ‘Entrez.GeneSybo.list’
DoFEMbi: no visible binding for global variable ‘toydata’
DoIntEpi450k: no visible binding for global variable ‘map450kEID.v’
DoIntEpi450k: no visible binding for global variable ‘probeInfoALL.lv’
DoIntFEM450k: no visible binding for global variable ‘map450kEID.v’
DoIntFEM450k: no visible binding for global variable ‘probeInfoALL.lv’
DoIntFEM450k: no visible binding for global variable
  ‘Entrez.GeneSybo.list’
* checking Rd files ... NOTE
prepare_Rd: DoEpiMod.Rd:53-55: Dropping empty section \details
prepare_Rd: DoEpiMod.Rd:56-62: Dropping empty section \value
prepare_Rd: DoEpiMod.Rd:69-71: Dropping empty section \note
prepare_Rd: DoEpiMod.Rd:66-68: Dropping empty section \author
prepare_Rd: DoEpiMod.Rd:63-65: Dropping empty section \references
prepare_Rd: DoEpiMod.Rd:75-77: Dropping empty section \seealso
prepare_Rd: DoExpMod.Rd:78: Dropping empty section \keyword
prepare_Rd: DoExpMod.Rd:79: Dropping empty section \keyword
prepare_Rd: DoExpMod.Rd:51-53: Dropping empty section \details
prepare_Rd: DoExpMod.Rd:54-60: Dropping empty section \value
prepare_Rd: DoExpMod.Rd:67-69: Dropping empty section \note
prepare_Rd: DoExpMod.Rd:64-66: Dropping empty section \author
prepare_Rd: DoExpMod.Rd:61-63: Dropping empty section \references
prepare_Rd: DoExpMod.Rd:73-75: Dropping empty section \seealso
prepare_Rd: DoExpMod.Rd:76-77: Dropping empty section \examples
prepare_Rd: DoFEMbi.Rd:54-56: Dropping empty section \details
prepare_Rd: DoFEMbi.Rd:57-63: Dropping empty section \value
prepare_Rd: DoFEMbi.Rd:70-72: Dropping empty section \note
prepare_Rd: DoFEMbi.Rd:67-69: Dropping empty section \author
prepare_Rd: DoFEMbi.Rd:64-66: Dropping empty section \references
prepare_Rd: DoFEMbi.Rd:76-78: Dropping empty section \seealso
prepare_Rd: DoIntEpi450k.Rd:34-36: Dropping empty section \details
prepare_Rd: DoIntEpi450k.Rd:37-43: Dropping empty section \value
prepare_Rd: DoIntEpi450k.Rd:50-52: Dropping empty section \note
prepare_Rd: DoIntEpi450k.Rd:47-49: Dropping empty section \author
prepare_Rd: DoIntEpi450k.Rd:44-46: Dropping empty section \references
prepare_Rd: DoIntEpi450k.Rd:56-58: Dropping empty section \seealso
prepare_Rd: DoIntExp.Rd:33-35: Dropping empty section \details
prepare_Rd: DoIntExp.Rd:36-42: Dropping empty section \value
prepare_Rd: DoIntExp.Rd:49-51: Dropping empty section \note
prepare_Rd: DoIntExp.Rd:46-48: Dropping empty section \author
prepare_Rd: DoIntExp.Rd:43-45: Dropping empty section \references
prepare_Rd: DoIntExp.Rd:55-57: Dropping empty section \seealso
prepare_Rd: DoIntExp.Rd:58-59: Dropping empty section \examples
prepare_Rd: DoIntFEM450k.Rd:38-40: Dropping empty section \details
prepare_Rd: DoIntFEM450k.Rd:41-47: Dropping empty section \value
prepare_Rd: DoIntFEM450k.Rd:54-56: Dropping empty section \note
prepare_Rd: DoIntFEM450k.Rd:51-53: Dropping empty section \author
prepare_Rd: DoIntFEM450k.Rd:48-50: Dropping empty section \references
prepare_Rd: DoIntFEM450k.Rd:60-62: Dropping empty section \seealso
prepare_Rd: DoIntFEM450k.Rd:63-65: Dropping empty section \examples
prepare_Rd: DoLimma.Rd:22-24: Dropping empty section \details
prepare_Rd: DoLimma.Rd:25-31: Dropping empty section \value
prepare_Rd: DoLimma.Rd:38-40: Dropping empty section \note
prepare_Rd: DoLimma.Rd:35-37: Dropping empty section \author
prepare_Rd: DoLimma.Rd:32-34: Dropping empty section \references
prepare_Rd: DoLimma.Rd:44-46: Dropping empty section \seealso
prepare_Rd: Entrez.GeneSybo.list.Rd:116-118: Dropping empty section \details
prepare_Rd: Entrez.GeneSybo.list.Rd:119-121: Dropping empty section \source
prepare_Rd: Entrez.GeneSybo.list.Rd:122-124: Dropping empty section \references
prepare_Rd: FEM-package.Rd:36-37: Dropping empty section \seealso
prepare_Rd: FEM-package.Rd:38-40: Dropping empty section \examples
prepare_Rd: FemModShow.Rd:34-36: Dropping empty section \details
prepare_Rd: FemModShow.Rd:37-43: Dropping empty section \value
prepare_Rd: FemModShow.Rd:50-52: Dropping empty section \note
prepare_Rd: FemModShow.Rd:47-49: Dropping empty section \author
prepare_Rd: FemModShow.Rd:44-46: Dropping empty section \references
prepare_Rd: FemModShow.Rd:56-58: Dropping empty section \seealso
prepare_Rd: fembi.o.Rd:16-18: Dropping empty section \details
prepare_Rd: fembi.o.Rd:19-21: Dropping empty section \source
prepare_Rd: fembi.o.Rd:22-24: Dropping empty section \references
prepare_Rd: map450kEID.v.Rd:11-12: Dropping empty section \format
prepare_Rd: map450kEID.v.Rd:13-15: Dropping empty section \details
prepare_Rd: map450kEID.v.Rd:16-18: Dropping empty section \source
prepare_Rd: map450kEID.v.Rd:19-21: Dropping empty section \references
prepare_Rd: probeInfoALL.lv.Rd:11-12: Dropping empty section \format
prepare_Rd: probeInfoALL.lv.Rd:13-15: Dropping empty section \details
prepare_Rd: probeInfoALL.lv.Rd:16-18: Dropping empty section \source
prepare_Rd: probeInfoALL.lv.Rd:19-21: Dropping empty section \references
prepare_Rd: realdata.Rd:11-12: Dropping empty section \format
prepare_Rd: realdata.Rd:13-15: Dropping empty section \details
prepare_Rd: realdata.Rd:16-18: Dropping empty section \source
prepare_Rd: realdata.Rd:19-21: Dropping empty section \references
prepare_Rd: tennodes.Rd:12-13: Dropping empty section \format
prepare_Rd: tennodes.Rd:14-16: Dropping empty section \details
prepare_Rd: tennodes.Rd:17-19: Dropping empty section \source
prepare_Rd: tennodes.Rd:20-22: Dropping empty section \references
prepare_Rd: toydata.Rd:36-38: Dropping empty section \details
prepare_Rd: toydata.Rd:39-41: Dropping empty section \source
prepare_Rd: toydata.Rd:42-44: Dropping empty section \references
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
DoFEMbi    7.990  0.159   8.163
FemModShow 6.267  1.507   7.790
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [46s/46s]
 [46s/46s] 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

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/FEM.Rcheck/00check.log’
for details.

FEM.Rcheck/00install.out:

* installing *source* package ‘FEM’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FEM)

FEM.Rcheck/FEM-Ex.timings:

nameusersystemelapsed
DoEpiMod0.0010.0000.001
DoFEMbi7.9900.1598.163
DoIntEpi450k0.0010.0000.001
DoLimma000
Entrez.GeneSybo.list0.1260.0050.131
FemModShow6.2671.5077.790
fembi.o0.0570.0070.063
map450kEID.v0.8540.0550.909
probeInfoALL.lv0.8000.0820.882
realdata3.1410.5713.712
tennodes0.0020.0010.003
toydata0.0030.0010.003