Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:04:50 -0400 (Wed, 22 Sep 2021).

CHECK results for exomePeak2 on nebbiolo1

To the developers/maintainers of the exomePeak2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/exomePeak2.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 605/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
exomePeak2 1.4.2  (landing page)
Zhen Wei
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/exomePeak2
git_branch: RELEASE_3_13
git_last_commit: d8d75f9
git_last_commit_date: 2021-09-07 12:28:10 -0400 (Tue, 07 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: exomePeak2
Version: 1.4.2
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:exomePeak2.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings exomePeak2_1.4.2.tar.gz
StartedAt: 2021-09-21 09:51:43 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 09:58:21 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 398.9 seconds
RetCode: 0
Status:   OK  
CheckDir: exomePeak2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:exomePeak2.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings exomePeak2_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/exomePeak2.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘exomePeak2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exomePeak2’ version ‘1.4.2’
* package encoding: UTF-8
* 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 ‘exomePeak2’ 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
GLM_inference : <anonymous>: no visible global function definition for
  ‘median’
Results,SummarizedExomePeak: no visible global function definition for
  ‘glm_M’
estimateSeqDepth,SummarizedExomePeak : <anonymous>: no visible global
  function definition for ‘median’
exomePeakCalling,MeripBamFileList: no visible global function
  definition for ‘metadata’
exomePeakCalling,MeripBamFileList: no visible global function
  definition for ‘%over%’
plotLfcGC,SummarizedExomePeak: no visible binding for global variable
  ‘GC_idx’
plotLfcGC,SummarizedExomePeak: no visible binding for global variable
  ‘Log2FC’
plotLfcGC,SummarizedExomePeak: no visible binding for global variable
  ‘Label’
plotReadsGC,SummarizedExomePeak: no visible binding for global variable
  ‘GC_cont’
plotReadsGC,SummarizedExomePeak: no visible binding for global variable
  ‘value’
plotSizeFactors,SummarizedExomePeak: no visible binding for global
  variable ‘samples’
plotSizeFactors,SummarizedExomePeak: no visible binding for global
  variable ‘size_factors’
plotSizeFactors,SummarizedExomePeak: no visible binding for global
  variable ‘Estimation_Methods’
Undefined global functions or variables:
  %over% Estimation_Methods GC_cont GC_idx Label Log2FC glm_M median
  metadata samples size_factors value
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
exomePeak2                67.782  0.245  68.033
exomePeakCalling-methods  40.148  0.177  40.331
SummarizedExomePeak-class 22.900  0.299  23.226
glmM-methods               5.055  0.004   5.059
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/exomePeak2.Rcheck/00check.log’
for details.



Installation output

exomePeak2.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL exomePeak2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘exomePeak2’ ...
** using staged installation
** R
** 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 (exomePeak2)

Tests output


Example timings

exomePeak2.Rcheck/exomePeak2-Ex.timings

nameusersystemelapsed
GCsizeFactors-methods0.0480.0000.049
LibraryType-methods0.1760.0000.176
MeripBamFileList-class0.2060.0190.226
Parameter-methods0.0890.0130.101
Results-methods0.8300.1430.973
SummarizedExomePeak-class22.900 0.29923.226
estimateSeqDepth-methods0.1110.0000.111
exomePeak267.782 0.24568.033
exomePeak2Results-methods0.0060.0030.009
exomePeakCalling-methods40.148 0.17740.331
exportResults-methods1.1200.0031.124
glmDM-methods4.6000.0044.604
glmM-methods5.0550.0045.059
normalizeGC-methods0.1060.0030.110
plotExonLength-methods0.890.000.89
plotLfcGC-methods0.1590.0000.159
plotReadsGC-methods0.8960.0000.896
plotSizeFactors-methods0.3520.0040.357
scanMeripBAM0.1940.0000.194