Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 702/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fCI 1.36.0  (landing page)
Shaojun Tang
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/fCI
git_branch: RELEASE_3_20
git_last_commit: 2d75697
git_last_commit_date: 2024-10-29 10:02:06 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for fCI on palomino8

To the developers/maintainers of the fCI package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: fCI
Version: 1.36.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fCI.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings fCI_1.36.0.tar.gz
StartedAt: 2024-12-20 01:31:42 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 01:33:40 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 117.7 seconds
RetCode: 0
Status:   OK  
CheckDir: fCI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fCI.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings fCI_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/fCI.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'fCI/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fCI' version '1.36.0'
* checking package namespace information ... NOTE
Found export directives that require package 'methods':
  'exportClasses' 'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
* 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 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 code 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 ... NOTE
Argument items with no description in Rd file 'compute.Rd':
  '.Object'
Argument items with no description in Rd file 'figures.Rd':
  '.Object'
Argument items with no description in Rd file 'find.mid.point.Rd':
  'Y'
Argument items with no description in Rd file 'get.npci.data.Rd':
  'sample.data.normalized' 'wt.index' 'df.index'
Argument items with no description in Rd file 'get.npci.distance.matrix.Rd':
  'npci.data' 'null.data.start' 'diff.data.start' 'choice'
  'rank.index.to.be.removed' 'expr.by.fold' 'ctr.indexes' 'trt.indexes'
  'use.intersect' 'symmetric.fold' 'fold.cutoff.list'
Argument items with no description in Rd file 'get.outline.index.Rd':
  'values'
Argument items with no description in Rd file 'populate.Rd':
  '.Object'
* 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  5.78   0.33    6.11
fCI.call.by.index 3.45   2.58   50.03
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/fCI.Rcheck/00check.log'
for details.


Installation output

fCI.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL fCI
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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
** 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-class000
call.npci000
compute000
deg.pairwise.fold.change000
deg.up.down.info000
deseq.median.ratio.normalization0.020.000.02
divergence.multivariate.distributions0.000.000.04
fCI-class000
fCI.call.by.index 3.45 2.5850.03
figures000
find.fci.targets5.780.336.11
find.mid.point0.390.040.44
get.fold.large.step000
get.npci.data000
get.npci.distance.matrix0.020.030.05
get.outline.index000
get.protein.fold.step000
get.rank.combinations000
get.rna.fold.step000
intersect.of.lists0.010.000.01
is.installed0.050.020.07
normalization000
npci.gene.by.pvalues000
npci.index.reconsidered0.230.000.23
npci.index.to.be.removed000
npci.venn.diagram0.180.030.24
pairwise.change.occupancy000
populate000
report.target.summary000
setfCI000
show.targets000
summarize0.010.000.01
total.library.size.normalization000
trim.size.normalization000
two.sample.log.ratio000
two.sample.permutation.test0.030.000.03
venndiagram000