Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:05:10 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for fCI on nebbiolo2


To the developers/maintainers of the fCI package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fCI.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 630/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fCI 1.24.0  (landing page)
Shaojun Tang
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/fCI
git_branch: RELEASE_3_14
git_last_commit: 1dbe6dd
git_last_commit_date: 2021-10-26 12:21:13 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: fCI
Version: 1.24.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:fCI.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings fCI_1.24.0.tar.gz
StartedAt: 2022-01-13 07:31:58 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 07:32:49 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 50.7 seconds
RetCode: 0
Status:   OK  
CheckDir: fCI.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:fCI.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings fCI_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/fCI.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.24.0’
* 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 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-3.14-bioc/meat/fCI.Rcheck/00check.log’
for details.



Installation output

fCI.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL fCI
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘fCI’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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
   ‘fCI.Rmd’ 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fCI)

Tests output


Example timings

fCI.Rcheck/fCI-Ex.timings

nameusersystemelapsed
NPCI-class0.0030.0000.003
call.npci0.0000.0000.001
compute000
deg.pairwise.fold.change0.0000.0000.001
deg.up.down.info000
deseq.median.ratio.normalization0.0070.0000.007
divergence.multivariate.distributions0.0070.0000.008
fCI-class0.0010.0000.001
fCI.call.by.index1.5970.2471.845
figures000
find.fci.targets3.7130.0523.765
find.mid.point0.2710.0040.276
get.fold.large.step0.0000.0000.001
get.npci.data0.0020.0000.001
get.npci.distance.matrix0.0190.0000.019
get.outline.index0.0040.0000.005
get.protein.fold.step0.0000.0000.001
get.rank.combinations0.0010.0000.001
get.rna.fold.step000
intersect.of.lists000
is.installed0.0320.0000.032
normalization000
npci.gene.by.pvalues0.0040.0000.003
npci.index.reconsidered0.1110.0000.111
npci.index.to.be.removed0.0010.0000.000
npci.venn.diagram0.1420.0040.145
pairwise.change.occupancy0.0010.0000.000
populate000
report.target.summary000
setfCI000
show.targets0.0000.0000.001
summarize0.0050.0000.005
total.library.size.normalization0.0030.0000.004
trim.size.normalization0.0040.0000.004
two.sample.log.ratio0.0010.0000.000
two.sample.permutation.test0.0320.0000.032
venndiagram000