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CHECK report for fCI on merida2

This page was generated on 2018-10-17 08:55:00 -0400 (Wed, 17 Oct 2018).

Package 482/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fCI 1.10.0
Shaojun Tang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/fCI
Branch: RELEASE_3_7
Last Commit: 2bc28ed
Last Changed Date: 2018-04-30 10:35:37 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  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: fCI
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fCI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fCI_1.10.0.tar.gz
StartedAt: 2018-10-16 21:19:51 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:20:39 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 47.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: fCI.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fCI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fCI_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/fCI.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 ‘fCI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fCI’ version ‘1.10.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.7-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 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 ... NOTE
fCI.call.by.index: no visible global function definition for ‘new’
fCI.call.by.index: no visible global function definition for
  ‘initialize’
find.fci.targets,NPCI: no visible global function definition for
  ‘initialize’
populate,NPCI: no visible global function definition for ‘.hasSlot’
populate,NPCI: no visible global function definition for ‘slot’
Undefined global functions or variables:
  .hasSlot initialize new slot
Consider adding
  importFrom("methods", ".hasSlot", "initialize", "new", "slot")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/fCI.Rcheck/00check.log’
for details.



Installation output

fCI.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL fCI
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘fCI’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
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 ‘setfCI’ 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
   ‘fCI.Rmd’ 
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (fCI)

Tests output


Example timings

fCI.Rcheck/fCI-Ex.timings

nameusersystemelapsed
NPCI-class0.0040.0010.003
call.npci0.0010.0000.002
compute0.0010.0000.002
deg.pairwise.fold.change0.0020.0000.003
deg.up.down.info0.0010.0000.002
deseq.median.ratio.normalization0.0110.0010.014
divergence.multivariate.distributions0.0090.0020.011
fCI-class0.0040.0010.004
fCI.call.by.index1.6030.1941.811
figures0.0010.0010.001
find.fci.targets3.3650.1883.571
find.mid.point0.4710.0290.504
get.fold.large.step0.0010.0000.001
get.npci.data0.0030.0010.003
get.npci.distance.matrix0.0310.0010.032
get.outline.index0.0150.0000.016
get.protein.fold.step0.0010.0000.002
get.rank.combinations0.0020.0000.002
get.rna.fold.step0.0010.0000.002
intersect.of.lists0.0010.0000.001
is.installed0.0290.0010.029
normalization0.0010.0000.002
npci.gene.by.pvalues0.0120.0010.012
npci.index.reconsidered0.1010.0030.105
npci.index.to.be.removed0.0010.0000.001
npci.venn.diagram0.1850.0180.207
pairwise.change.occupancy0.0030.0010.003
populate0.0010.0000.001
report.target.summary0.0010.0000.002
setfCI0.0020.0000.001
show.targets0.0010.0000.004
summarize0.0140.0060.020
total.library.size.normalization0.0060.0010.007
trim.size.normalization0.0060.0020.008
two.sample.log.ratio0.0010.0000.001
two.sample.permutation.test0.0250.0000.024
venndiagram0.0010.0000.001