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BioC 3.4: CHECK report for fCI on zin1

This page was generated on 2016-09-21 03:40:00 -0700 (Wed, 21 Sep 2016).

Package 398/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fCI 1.3.2
Shaojun Tang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/fCI
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: fCI
Version: 1.3.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings fCI_1.3.2.tar.gz
StartedAt: 2016-09-20 06:19:57 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:20:29 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 31.5 seconds
RetCode: 0
Status:  OK 
CheckDir: fCI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings fCI_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/fCI.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.3.2’
* 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
* 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-3.4-bioc/meat/fCI.Rcheck/00check.log’
for details.


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)

fCI.Rcheck/fCI-Ex.timings:

nameusersystemelapsed
NPCI-class0.0000.0000.002
call.npci0.0000.0000.001
compute000
deg.pairwise.fold.change0.0000.0000.001
deg.up.down.info0.0000.0000.001
deseq.median.ratio.normalization0.0040.0000.007
divergence.multivariate.distributions0.0040.0000.005
fCI-class0.0000.0000.001
fCI.call.by.index0.6960.0280.726
figures000
find.fci.targets2.1920.0202.209
find.mid.point0.3440.0000.345
get.fold.large.step0.0000.0000.001
get.npci.data0.0000.0000.001
get.npci.distance.matrix0.0240.0000.027
get.outline.index0.0040.0000.008
get.protein.fold.step000
get.rank.combinations0.0000.0000.001
get.rna.fold.step0.0000.0000.001
intersect.of.lists000
is.installed0.0120.0000.012
normalization0.0000.0000.001
npci.gene.by.pvalues0.0040.0000.007
npci.index.reconsidered0.0600.0000.063
npci.index.to.be.removed000
npci.venn.diagram0.3080.0120.322
pairwise.change.occupancy0.0000.0000.001
populate0.0000.0000.001
report.target.summary0.0000.0000.001
setfCI000
show.targets0.0000.0000.001
summarize0.0080.0000.006
total.library.size.normalization0.0040.0000.005
trim.size.normalization0.0040.0000.005
two.sample.log.ratio000
two.sample.permutation.test0.0360.0000.034
venndiagram0.0000.0000.001