Back to Build/check report for BioC 3.17
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2023-01-02 09:00:37 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 MEDIPS on palomino5


To the developers/maintainers of the MEDIPS package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1109/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEDIPS 1.51.0  (landing page)
Lukas Chavez
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/MEDIPS
git_branch: master
git_last_commit: b841cb0
git_last_commit_date: 2022-11-01 11:05:24 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: MEDIPS
Version: 1.51.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEDIPS.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MEDIPS_1.51.0.tar.gz
StartedAt: 2022-12-29 01:07:44 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 01:12:38 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 294.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MEDIPS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEDIPS.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MEDIPS_1.51.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MEDIPS.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.51.0'
* 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 'MEDIPS' 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
MEDIPS.CpGenrich: no visible global function definition for 'seqlevels'
MEDIPS.CpGenrich: no visible global function definition for
  'seqlengths'
MEDIPS.CpGenrich: no visible global function definition for
  'GRangesList'
MEDIPS.CpGenrich : <anonymous>: no visible global function definition
  for 'seqnames'
MEDIPS.CpGenrich: no visible global function definition for 'new'
MEDIPS.addCNV: no visible global function definition for 'seqnames'
MEDIPS.correlation: no visible global function definition for 'pdf'
MEDIPS.correlation: no visible global function definition for 'dev.off'
MEDIPS.couplingVector: no visible global function definition for 'new'
MEDIPS.createROIset: no visible global function definition for
  'seqnames'
MEDIPS.createROIset: no visible global function definition for
  'seqlengths'
MEDIPS.createROIset: no visible global function definition for 'new'
MEDIPS.createSet: no visible global function definition for 'seqnames'
MEDIPS.createSet: no visible global function definition for
  'seqlengths'
MEDIPS.createSet: no visible global function definition for 'seqlevels'
MEDIPS.createSet: no visible global function definition for 'new'
MEDIPS.diffMeth: no visible global function definition for 'p.adjust'
MEDIPS.exportWIG: no visible global function definition for 'seqnames'
MEDIPS.mergeSets: no visible global function definition for 'new'
MEDIPS.meth: no visible global function definition for 'seqnames'
MEDIPS.plotCalibrationPlot: no visible global function definition for
  'seqnames'
MEDIPS.plotCalibrationPlot: no visible global function definition for
  'points'
MEDIPS.plotSeqCoverage: no visible global function definition for 'pie'
MEDIPS.plotSeqCoverage: no visible global function definition for
  'hist'
MEDIPS.saturation: no visible global function definition for
  'seqlevels'
MEDIPS.saturation: no visible global function definition for
  'seqlengths'
MEDIPS.selectROIs: no visible global function definition for
  'elementMetadata<-'
MEDIPS.selectROIs: no visible global function definition for
  'elementMetadata'
MEDIPS.selectROIs: no visible global function definition for
  'findOverlaps'
MEDIPS.selectROIs: no visible global function definition for 'values'
MEDIPS.selectROIs: no visible global function definition for 'seqnames'
MEDIPS.seqCoverage: no visible global function definition for
  'seqlevels'
MEDIPS.seqCoverage: no visible global function definition for
  'seqlengths'
MEDIPS.setAnnotation: no visible global function definition for
  'findOverlaps'
MEDIPS.setAnnotation: no visible global function definition for
  'values'
getGRange: no visible global function definition for 'qpois'
getGRange: no visible global function definition for 'seqlengths'
getGRange: no visible global function definition for 'countMatches'
getGRange: no visible global function definition for 'strand<-'
getMObjectFromWIG: no visible global function definition for
  'seqlengths'
getMObjectFromWIG: no visible global function definition for 'values'
getMObjectFromWIG: no visible global function definition for
  'runLength'
getMObjectFromWIG: no visible global function definition for 'seqnames'
getMObjectFromWIG: no visible global function definition for 'runValue'
getMObjectFromWIG: no visible global function definition for 'new'
getPairedGRange: no visible global function definition for 'sd'
getPairedGRange: no visible global function definition for 'qpois'
getPairedGRange: no visible global function definition for 'seqlengths'
getPairedGRange: no visible global function definition for
  'countMatches'
getPairedGRange: no visible global function definition for 'strand<-'
matSd: no visible binding for global variable 'sd'
matTtest: no visible binding for global variable 'sd'
matTtest: no visible global function definition for 'pt'
Undefined global functions or variables:
  GRangesList countMatches dev.off elementMetadata elementMetadata<-
  findOverlaps hist new p.adjust pdf pie points pt qpois runLength
  runValue sd seqlengths seqlevels seqnames strand<- values
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "hist", "pie", "points")
  importFrom("methods", "new")
  importFrom("stats", "p.adjust", "pt", "qpois", "sd")
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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
MEDIPS.meth   38.23   0.97   39.27
MEDIPS.addCNV 19.63   0.29   20.23
* 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 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MEDIPS.Rcheck/00check.log'
for details.



Installation output

MEDIPS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL MEDIPS
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'MEDIPS' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for request: 'values' when loading 'MEDIPS'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'IRanges' for request: 'values' when loading 'MEDIPS'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for request: 'values' when loading 'MEDIPS'
** testing if installed package keeps a record of temporary installation path
* DONE (MEDIPS)

Tests output


Example timings

MEDIPS.Rcheck/MEDIPS-Ex.timings

nameusersystemelapsed
COUPLINGset-class000
MEDIPS.CpGenrich0.030.000.08
MEDIPS.addCNV19.63 0.2920.23
MEDIPS.correlation1.060.081.14
MEDIPS.couplingVector4.300.084.39
MEDIPS.createROIset0.940.010.95
MEDIPS.createSet0.920.070.99
MEDIPS.exportWIG1.890.081.97
MEDIPS.getAnnotation000
MEDIPS.mergeFrames0.020.000.01
MEDIPS.mergeSets0.630.010.66
MEDIPS.meth38.23 0.9739.27
MEDIPS.plotCalibrationPlot2.890.082.96
MEDIPS.plotSaturation4.770.204.97
MEDIPS.plotSeqCoverage4.140.084.22
MEDIPS.saturation4.420.234.66
MEDIPS.selectROIs1.400.021.42
MEDIPS.selectSig1.850.051.89
MEDIPS.seqCoverage4.360.064.42
MEDIPS.setAnnotation1.810.091.91
MEDIPSroiSet-class000
MEDIPSset-class000