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This page was generated on 2024-02-22 12:48:42 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
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 1215/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylPipe 1.37.0  (landing page)
Mattia Furlan
Snapshot Date: 2024-02-21 14:10:10 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/methylPipe
git_branch: devel
git_last_commit: 9fa1f0e
git_last_commit_date: 2023-10-24 10:00:55 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for methylPipe on palomino3


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: 1.37.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylPipe.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings methylPipe_1.37.0.tar.gz
StartedAt: 2024-02-22 05:07:15 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 05:15:45 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 510.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: methylPipe.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylPipe.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings methylPipe_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/methylPipe.Rcheck'
* using R Under development (unstable) (2024-01-14 r85805 ucrt)
* using platform: x86_64-w64-mingw32
* 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 'methylPipe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methylPipe' version '1.37.0'
* 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 'methylPipe' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* 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 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 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 ... OK
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/methylPipe/libs/x64/methylPipe.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'F:/biocbuild/bbs-3.19-bioc/tmpdir/Rtmpo9MDUt', resetting
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
plotMeth           22.22   1.09   62.94
findDMR             1.20   1.80   31.64
GEcollection-class  2.83   0.16    5.89
methstats           0.97   0.24   20.98
findPMDs            0.16   0.17   23.13
* 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: 2 WARNINGs, 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/methylPipe.Rcheck/00check.log'
for details.



Installation output

methylPipe.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL methylPipe
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'methylPipe' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_methylPipe.c -o R_init_methylPipe.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c binning.c -o binning.o
gcc -shared -s -static-libgcc -o methylPipe.dll tmp.def R_init_methylPipe.o binning.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-methylPipe/00new/methylPipe/libs/x64
** 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
** 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-class0.310.010.34
BSdataSet-class0.160.040.21
BSprepare000
GEcollection-class2.830.165.89
GElist-class0.030.000.05
chiCombP000
consolidateDMRs0.280.000.30
extractBinGRanges0.020.030.04
findDMR 1.20 1.8031.64
findPMDs 0.16 0.1723.13
getCpos0.090.030.12
getCposDensity0.080.030.11
mCsmoothing0.340.020.36
mapBSdata2GRanges0.990.041.06
methstats 0.97 0.2420.98
plotMeth22.22 1.0962.94
pool.reads000
process.hmc000
profileDNAmetBin1.320.171.50