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This page was generated on 2021-10-22 12:04:32 -0400 (Fri, 22 Oct 2021).

CHECK results for MEDIPS on riesling1

To the developers/maintainers of the MEDIPS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MEDIPS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1073/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEDIPS 1.45.0  (landing page)
Lukas Chavez
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/MEDIPS
git_branch: master
git_last_commit: ad46924
git_last_commit_date: 2021-05-19 11:46:46 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: MEDIPS
Version: 1.45.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEDIPS.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MEDIPS_1.45.0.tar.gz
StartedAt: 2021-10-22 01:52:23 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 01:59:05 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 401.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MEDIPS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEDIPS.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MEDIPS_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/MEDIPS.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.45.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
MEDIPS.meth   33.45   1.28   34.75
MEDIPS.addCNV 18.55   0.52   19.30
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
MEDIPS.meth           30.83   1.56   32.39
MEDIPS.addCNV         17.83   0.42   18.25
MEDIPS.saturation      5.00   0.31    5.31
MEDIPS.plotSaturation  4.76   0.46    5.22
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/MEDIPS.Rcheck/00check.log'
for details.



Installation output

MEDIPS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MEDIPS_1.45.0.tar.gz && rm -rf MEDIPS.buildbin-libdir && mkdir MEDIPS.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MEDIPS.buildbin-libdir MEDIPS_1.45.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MEDIPS_1.45.0.zip && rm MEDIPS_1.45.0.tar.gz MEDIPS_1.45.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 61288    1  1139    0     0  13722      0  0:00:04 --:--:--  0:00:04 13559
100 61288  100 61288    0     0   391k      0 --:--:-- --:--:-- --:--:--  388k

install for i386

* 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
  converting help for package 'MEDIPS'
    finding HTML links ... done
    COUPLINGset-class                       html  
    MEDIPS-package                          html  
    MEDIPS.CpGenrich                        html  
    MEDIPS.addCNV                           html  
    MEDIPS.correlation                      html  
    MEDIPS.couplingVector                   html  
    MEDIPS.createROIset                     html  
    MEDIPS.createSet                        html  
    MEDIPS.exportWIG                        html  
    MEDIPS.getAnnotation                    html  
    MEDIPS.mergeFrames                      html  
    MEDIPS.mergeSets                        html  
    MEDIPS.meth                             html  
    MEDIPS.plotCalibrationPlot              html  
    MEDIPS.plotSaturation                   html  
    MEDIPS.plotSeqCoverage                  html  
    MEDIPS.saturation                       html  
    MEDIPS.selectROIs                       html  
    MEDIPS.selectSig                        html  
    MEDIPS.seqCoverage                      html  
    MEDIPS.setAnnotation                    html  
    MEDIPSroiSet-class                      html  
    MEDIPSset-class                         html  
** 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

install for x64

* installing *source* package 'MEDIPS' ...
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'values' when loading 'MEDIPS'
* MD5 sums
packaged installation of 'MEDIPS' as MEDIPS_1.45.0.zip
* DONE (MEDIPS)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'MEDIPS' successfully unpacked and MD5 sums checked

Tests output


Example timings

MEDIPS.Rcheck/examples_i386/MEDIPS-Ex.timings

nameusersystemelapsed
COUPLINGset-class000
MEDIPS.CpGenrich0.030.000.03
MEDIPS.addCNV18.55 0.5219.30
MEDIPS.correlation1.000.061.06
MEDIPS.couplingVector2.900.093.00
MEDIPS.createROIset0.970.020.98
MEDIPS.createSet0.880.020.89
MEDIPS.exportWIG1.670.011.69
MEDIPS.getAnnotation000
MEDIPS.mergeFrames0.020.000.01
MEDIPS.mergeSets0.530.020.60
MEDIPS.meth33.45 1.2834.75
MEDIPS.plotCalibrationPlot2.720.082.79
MEDIPS.plotSaturation4.560.424.99
MEDIPS.plotSeqCoverage2.640.062.70
MEDIPS.saturation4.360.444.79
MEDIPS.selectROIs1.370.031.41
MEDIPS.selectSig2.550.172.72
MEDIPS.seqCoverage2.780.082.86
MEDIPS.setAnnotation2.590.132.72
MEDIPSroiSet-class000
MEDIPSset-class000

MEDIPS.Rcheck/examples_x64/MEDIPS-Ex.timings

nameusersystemelapsed
COUPLINGset-class000
MEDIPS.CpGenrich0.030.000.03
MEDIPS.addCNV17.83 0.4218.25
MEDIPS.correlation1.060.051.11
MEDIPS.couplingVector3.110.073.18
MEDIPS.createROIset0.910.020.93
MEDIPS.createSet0.950.010.96
MEDIPS.exportWIG1.800.041.83
MEDIPS.getAnnotation000
MEDIPS.mergeFrames000
MEDIPS.mergeSets0.610.010.63
MEDIPS.meth30.83 1.5632.39
MEDIPS.plotCalibrationPlot2.940.113.05
MEDIPS.plotSaturation4.760.465.22
MEDIPS.plotSeqCoverage2.790.122.91
MEDIPS.saturation5.000.315.31
MEDIPS.selectROIs1.030.071.09
MEDIPS.selectSig1.700.151.86
MEDIPS.seqCoverage2.770.112.87
MEDIPS.setAnnotation2.290.202.50
MEDIPSroiSet-class0.020.000.02
MEDIPSset-class000