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This page was generated on 2025-08-07 12:05 -0400 (Thu, 07 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1248/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylPipe 1.43.1  (landing page)
Mattia Furlan
Snapshot Date: 2025-08-06 14:04 -0400 (Wed, 06 Aug 2025)
git_url: https://git.bioconductor.org/packages/methylPipe
git_branch: devel
git_last_commit: c62f76a
git_last_commit_date: 2025-07-23 12:44:03 -0400 (Wed, 23 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for methylPipe on nebbiolo2

To the developers/maintainers of the methylPipe package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylPipe.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: methylPipe
Version: 1.43.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings methylPipe_1.43.1.tar.gz
StartedAt: 2025-08-07 00:12:36 -0400 (Thu, 07 Aug 2025)
EndedAt: 2025-08-07 00:22:21 -0400 (Thu, 07 Aug 2025)
EllapsedTime: 585.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: methylPipe.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings methylPipe_1.43.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/methylPipe.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘methylPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylPipe’ version ‘1.43.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘methylPipe’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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
findPMDs,BSdata : PMDchr: no visible global function definition for
  'segmentPMDs'
show,BSdata: no visible global function definition for 'organism'
show,BSdataSet: no visible global function definition for 'organism'
Undefined global functions or variables:
  organism segmentPMDs
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BSdata-class.Rd: GRanges
  GEcollection-class.Rd: RangedSummarizedExperiment, GRanges
  consolidateDMRs.Rd: GRanges
  extractBinGRanges.Rd: GRanges
  findDMR.Rd: GRanges
  getCpos.Rd: GRanges, DNAString
  getCposDensity.Rd: GRanges
  mapBSdata2GRanges.Rd: GRanges
  meth.call.Rd: GRanges
  plotMeth.Rd: GRanges, GRangesList
  process.hmc.Rd: GRanges, coverage, GenomicRanges
  profileDNAmetBin.Rd: GRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'BSdataSet,ANY,ANY,ANY'
  generic '[' and siglist 'GElist,ANY,ANY,ANY'
  generic '[[<-' and siglist 'BSdataSet,ANY,ANY,ANY'
  generic '[[<-' and siglist 'GElist,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to '/tmp/Rtmp7BR02B', resetting
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
plotMeth  24.005  3.463  32.263
findDMR    0.954  1.024  33.424
methstats  0.837  0.234  22.031
findPMDs   0.188  0.094  23.035
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/methylPipe.Rcheck/00check.log’
for details.


Installation output

methylPipe.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL methylPipe
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘methylPipe’ ...
** this is package ‘methylPipe’ version ‘1.43.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_methylPipe.c -o R_init_methylPipe.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c binning.c -o binning.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o methylPipe.so R_init_methylPipe.o binning.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-methylPipe/00new/methylPipe/libs
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (methylPipe)

Tests output


Example timings

methylPipe.Rcheck/methylPipe-Ex.timings

nameusersystemelapsed
BSdata-class0.1960.0050.201
BSdataSet-class0.1450.0030.147
BSprepare000
GEcollection-class3.1550.1363.293
GElist-class0.0330.0010.034
chiCombP0.0010.0000.000
consolidateDMRs0.2020.0080.210
extractBinGRanges0.0230.0010.025
findDMR 0.954 1.02433.424
findPMDs 0.188 0.09423.035
getCpos0.1510.0450.195
getCposDensity0.1100.0360.146
mCsmoothing0.3210.1410.462
mapBSdata2GRanges1.1240.1501.275
methstats 0.837 0.23422.031
plotMeth24.005 3.46332.263
pool.reads000
process.hmc000
profileDNAmetBin1.2910.0981.389