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BioC 3.2: CHECK report for fCI on perceval

This page was generated on 2015-11-10 14:49:57 -0800 (Tue, 10 Nov 2015).

Package 338/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fCI 1.0.0
Shaojun Tang
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/fCI
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: fCI
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings fCI_1.0.0.tar.gz
StartedAt: 2015-11-10 04:41:05 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 04:41:45 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 40.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: fCI.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings fCI_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/fCI.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fCI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fCI’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘FNN’ ‘psych’ ‘gtools’ ‘zoo’ ‘rgl’ ‘grid’ ‘VennDiagram’
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 ‘fCI’ can be installed ... [3s/3s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘gtools::logit’ when loading ‘fCI’
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/fCI.Rcheck/00install.out’ for details.
* 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
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘NPCI’
Undocumented S4 methods:
  generic 'find.fci.targets' and siglist 'NPCI'
  generic 'show.targets' and siglist 'NPCI'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/4s] 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/fCI.Rcheck/00check.log’
for details.


fCI.Rcheck/00install.out:

* installing *source* package ‘fCI’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
Warning: replacing previous import by ‘gtools::logit’ when loading ‘fCI’
in method for ‘initialize’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘normalization’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘populate’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘find.fci.targets’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘show.targets’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘call.npci’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘compute’ with signature ‘"NPCI"’: no definition for class “NPCI”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
Warning: replacing previous import by ‘gtools::logit’ when loading ‘fCI’
* DONE (fCI)

fCI.Rcheck/fCI-Ex.timings:

nameusersystemelapsed
call.npci0.0010.0000.001
compute0.0010.0000.000
deg.pairwise.fold.change0.0010.0000.001
deg.up.down.info000
deseq.median.ratio.normalization0.010.000.01
divergence.multivariate.distributions0.0070.0000.007
fCI-class0.0030.0010.004
fCI.call.by.index0.8920.0800.972
figures0.0010.0000.001
find.fci.targets0.0010.0000.000
find.mid.point0.5410.0140.556
get.fold.large.step0.0000.0000.001
get.npci.data0.0020.0010.003
get.npci.distance.matrix0.0370.0010.037
get.outline.index0.0120.0000.011
get.protein.fold.step0.0010.0000.001
get.rank.combinations0.0020.0000.003
get.rna.fold.step0.0010.0010.001
intersect.of.lists0.0000.0000.001
is.installed0.0160.0010.016
normalization0.0010.0000.000
npci.gene.by.pvalues0.0100.0010.010
npci.index.reconsidered0.0840.0020.085
npci.index.to.be.removed0.0010.0000.001
npci.venn.diagram0.4620.0260.592
pairwise.change.occupancy0.0020.0000.002
populate0.0000.0000.001
report.target.summary0.0000.0000.001
show.targets0.0010.0000.001
summarize0.0070.0000.008
total.library.size.normalization0.0070.0010.009
trim.size.normalization0.0070.0020.009
two.sample.log.ratio0.0000.0000.001
two.sample.permutation.test0.0480.0030.053
venndiagram0.0000.0000.001