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This page was generated on 2024-02-20 11:36:41 -0500 (Tue, 20 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4690
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4443
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4464
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 414/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compEpiTools 1.36.0  (landing page)
Mattia Furlan
Snapshot Date: 2024-02-19 14:05:07 -0500 (Mon, 19 Feb 2024)
git_url: https://git.bioconductor.org/packages/compEpiTools
git_branch: RELEASE_3_18
git_last_commit: a66a836
git_last_commit_date: 2023-10-24 10:00:44 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for compEpiTools on palomino4


To the developers/maintainers of the compEpiTools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/compEpiTools.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: compEpiTools
Version: 1.36.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:compEpiTools.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings compEpiTools_1.36.0.tar.gz
StartedAt: 2024-02-20 00:31:49 -0500 (Tue, 20 Feb 2024)
EndedAt: 2024-02-20 00:38:57 -0500 (Tue, 20 Feb 2024)
EllapsedTime: 427.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: compEpiTools.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:compEpiTools.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings compEpiTools_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/compEpiTools.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'compEpiTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compEpiTools' version '1.36.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'compEpiTools' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TSS: no visible global function definition for 'end<-'
TSS: no visible global function definition for 'start<-'
findLncRNA: no visible global function definition for 'start<-'
findLncRNA: no visible global function definition for 'end<-'
findLncRNA: no visible global function definition for 'IRanges'
stallingIndex : getBound: no visible global function definition for
  'start<-'
stallingIndex : getBound: no visible global function definition for
  'end<-'
stallingIndex: no visible global function definition for 'IRanges'
topGOres : <anonymous>: no visible global function definition for
  'ggplot'
topGOres : <anonymous>: no visible global function definition for 'aes'
topGOres : <anonymous>: no visible binding for global variable
  'Significant'
topGOres : <anonymous>: no visible binding for global variable 'P_val'
topGOres : <anonymous>: no visible global function definition for
  'geom_bar'
topGOres : <anonymous>: no visible global function definition for
  'coord_flip'
topGOres : <anonymous>: no visible global function definition for
  'ylab'
ucsc2GRanges: no visible global function definition for 'IRanges'
GR2fasta,GRanges: no visible global function definition for
  'seqlengths'
GR2fasta,GRanges: no visible global function definition for
  'seqlengths<-'
GR2fasta,GRanges: no visible global function definition for 'trim'
GRangesInPromoters,GRanges: no visible global function definition for
  'start<-'
GRannotate,GRanges: no visible global function definition for 'start<-'
GRannotate,GRanges: no visible global function definition for 'end<-'
GRcoverageSummit,GRanges: no visible global function definition for
  'start<-'
GRcoverageSummit,GRanges: no visible global function definition for
  'end<-'
GRmidpoint,GRanges: no visible global function definition for 'start<-'
GRmidpoint,GRanges: no visible global function definition for 'end<-'
GRsetwidth,GRanges: no visible global function definition for 'start<-'
GRsetwidth,GRanges: no visible global function definition for 'end<-'
countOverlapsInBins,GRanges: no visible global function definition for
  'IRanges'
featuresLength,TxDb: no visible global function definition for 'reduce'
getPromoterClass,TxDb: no visible binding for global variable 'txdb'
getPromoterClass,TxDb: no visible global function definition for
  'start<-'
makeGtfFromDb,TxDb: no visible global function definition for 'reduce'
matchEnhancers,GRanges: no visible global function definition for
  'distanceToNearest'
matchEnhancers,GRanges: no visible global function definition for
  'IRanges'
Undefined global functions or variables:
  IRanges P_val Significant aes coord_flip distanceToNearest end<-
  geom_bar ggplot reduce seqlengths seqlengths<- start<- trim txdb ylab
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'applyPileups' is deprecated.
  Warning: 'applyPileups' is deprecated.
  Warning: 'applyPileups' is deprecated.
  Warning: 'applyPileups' is deprecated.
  Warning: 'applyPileups' is deprecated.
  Warning: 'applyPileups' is deprecated.
  Warning: 'applyPileups' is deprecated.
  Warning: 'applyPileups' is deprecated.
  Warning: 'applyPileups' is deprecated.
  Warning: 'applyPileups' is deprecated.
  Warning: 'applyPileups' is deprecated.
  Warning: 'applyPileups' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
topGOres                 26.33   1.29   27.64
getPromoterClass-methods  0.73   0.04   18.92
* 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: 1 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.18-bioc/meat/compEpiTools.Rcheck/00check.log'
for details.



Installation output

compEpiTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL compEpiTools
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'compEpiTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (compEpiTools)

Tests output


Example timings

compEpiTools.Rcheck/compEpiTools-Ex.timings

nameusersystemelapsed
GR2fasta-methods0.520.050.62
GRanges2ucsc-methods0.010.000.02
GRangesInPromoters-methods2.990.073.06
GRannotate-methods4.080.084.20
GRannotateSimple0.580.020.60
GRbaseCoverage-methods0.060.030.11
GRcoverage-methods0.120.000.12
GRcoverageSummit-methods0.070.000.06
GRenrichment-methods0.070.000.08
GRmidpoint-methods0.100.000.09
GRsetwidth0.030.000.03
TSS2.360.022.38
countOverlapsInBins-methods0.110.000.11
distanceFromTSS-methods1.610.071.69
enhancers0.320.020.34
findLncRNA0.600.080.71
getPromoterClass-methods 0.73 0.0418.92
heatmapData0.990.041.01
heatmapPlot2.470.212.93
makeGtfFromDb2.750.163.20
matchEnhancers1.530.061.59
overlapOfGRanges-methods0.050.000.05
palette2d0.030.000.03
plotStallingIndex2.290.022.32
simplifyGOterms0.390.110.98
stallingIndex2.140.052.19
topGOres26.33 1.2927.64
ucsc2GRanges0.020.000.01
unionMaxScore-methods0.110.000.11