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CHECK report for fCI on malbec1

This page was generated on 2018-04-12 13:13:48 -0400 (Thu, 12 Apr 2018).

Package 458/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fCI 1.8.0
Shaojun Tang
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/fCI
Branch: RELEASE_3_6
Last Commit: 6eefcfd
Last Changed Date: 2017-10-30 12:40:52 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: fCI
Version: 1.8.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings fCI_1.8.0.tar.gz
StartedAt: 2018-04-11 23:25:00 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:25:56 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 56.0 seconds
RetCode: 0
Status:  OK 
CheckDir: fCI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings fCI_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/fCI.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.0’
* 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 ... 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
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
Examples with CPU or elapsed time > 5s
                   user system elapsed
fCI.call.by.index 1.564  0.188  19.437
* 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/fCI.Rcheck/00check.log’
for details.



Installation output

fCI.Rcheck/00install.out

* installing *source* package ‘fCI’ ...
** R
** data
** inst
** preparing package for lazy loading
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
** testing if installed package can be loaded
* DONE (fCI)

Tests output


Example timings

fCI.Rcheck/fCI-Ex.timings

nameusersystemelapsed
NPCI-class0.0000.0000.002
call.npci0.0000.0000.001
compute0.0040.0000.000
deg.pairwise.fold.change000
deg.up.down.info000
deseq.median.ratio.normalization0.0120.0000.009
divergence.multivariate.distributions0.0040.0000.007
fCI-class0.0000.0000.002
fCI.call.by.index 1.564 0.18819.437
figures000
find.fci.targets2.9080.0082.919
find.mid.point0.5040.0000.503
get.fold.large.step0.0000.0000.001
get.npci.data0.0000.0000.002
get.npci.distance.matrix0.0320.0000.030
get.outline.index0.0080.0000.007
get.protein.fold.step0.0000.0000.001
get.rank.combinations0.0000.0000.001
get.rna.fold.step0.0000.0000.001
intersect.of.lists0.0000.0000.001
is.installed0.0160.0000.013
normalization000
npci.gene.by.pvalues0.0040.0000.005
npci.index.reconsidered0.0640.0000.063
npci.index.to.be.removed0.0000.0000.001
npci.venn.diagram0.3240.0080.348
pairwise.change.occupancy0.0000.0000.001
populate0.0000.0040.001
report.target.summary000
setfCI000
show.targets000
summarize0.0040.0000.005
total.library.size.normalization0.0040.0000.004
trim.size.normalization0.0000.0040.004
two.sample.log.ratio0.0040.0000.000
two.sample.permutation.test0.0200.0000.022
venndiagram0.0040.0000.000