Back to Multiple platform build/check report for BioC 3.15
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-15 11:11:19 -0500 (Sat, 15 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4160
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4055
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3997
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4114
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 merida1


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 628/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fCI 1.25.0  (landing page)
Shaojun Tang
Snapshot Date: 2022-01-14 13:55:18 -0500 (Fri, 14 Jan 2022)
git_url: https://git.bioconductor.org/packages/fCI
git_branch: master
git_last_commit: 76cc2d1
git_last_commit_date: 2021-10-26 12:21:13 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: fCI
Version: 1.25.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fCI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fCI_1.25.0.tar.gz
StartedAt: 2022-01-15 00:44:28 -0500 (Sat, 15 Jan 2022)
EndedAt: 2022-01-15 00:45:36 -0500 (Sat, 15 Jan 2022)
EllapsedTime: 67.9 seconds
RetCode: 0
Status:   OK  
CheckDir: fCI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fCI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fCI_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/fCI.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.25.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
find.fci.targets 6.679  0.126   6.813
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/fCI.Rcheck/00check.log’
for details.



Installation output

fCI.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL fCI
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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
** 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-class0.0030.0010.004
call.npci000
compute0.0010.0000.001
deg.pairwise.fold.change0.0000.0000.001
deg.up.down.info000
deseq.median.ratio.normalization0.0800.0010.081
divergence.multivariate.distributions0.0110.0010.011
fCI-class0.0010.0010.002
fCI.call.by.index2.9700.5813.555
figures000
find.fci.targets6.6790.1266.813
find.mid.point0.5400.0190.559
get.fold.large.step000
get.npci.data0.0020.0020.003
get.npci.distance.matrix0.0410.0010.042
get.outline.index0.0120.0010.011
get.protein.fold.step0.0000.0000.001
get.rank.combinations0.0020.0000.002
get.rna.fold.step0.0000.0010.001
intersect.of.lists0.0000.0000.001
is.installed0.0630.0010.064
normalization0.0010.0010.000
npci.gene.by.pvalues0.0090.0000.010
npci.index.reconsidered0.2250.0030.228
npci.index.to.be.removed0.0000.0000.001
npci.venn.diagram0.2220.0210.248
pairwise.change.occupancy0.0010.0000.001
populate0.0010.0010.000
report.target.summary000
setfCI0.0010.0000.001
show.targets0.0010.0000.000
summarize0.0090.0010.010
total.library.size.normalization0.0060.0020.008
trim.size.normalization0.0050.0020.007
two.sample.log.ratio000
two.sample.permutation.test0.0690.0030.072
venndiagram0.0010.0000.000