Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-13 15:05:22 -0400 (Wed, 13 Oct 2021).

CHECK results for exomePeak2 on tokay2

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
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raw results

Package 605/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
exomePeak2 1.4.2  (landing page)
Zhen Wei
Snapshot Date: 2021-10-12 04:50:13 -0400 (Tue, 12 Oct 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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomePeak2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings exomePeak2_1.4.2.tar.gz
StartedAt: 2021-10-12 22:35:31 -0400 (Tue, 12 Oct 2021)
EndedAt: 2021-10-12 22:47:18 -0400 (Tue, 12 Oct 2021)
EllapsedTime: 706.9 seconds
RetCode: 0
Status:   OK  
CheckDir: exomePeak2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomePeak2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings exomePeak2_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/exomePeak2.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 '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 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
* 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
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
exomePeak2                81.67   0.29   83.14
exomePeakCalling-methods  42.69   0.17   43.20
SummarizedExomePeak-class 26.20   1.96   28.82
glmDM-methods              5.34   0.00    5.46
glmM-methods               5.22   0.00    5.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
exomePeak2                78.28   0.12   78.42
exomePeakCalling-methods  46.42   0.11   46.54
SummarizedExomePeak-class 27.84   1.03   28.88
glmDM-methods              5.47   0.00    5.47
glmM-methods               5.36   0.02    5.38
* 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/exomePeak2.Rcheck/00check.log'
for details.



Installation output

exomePeak2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/exomePeak2_1.4.2.tar.gz && rm -rf exomePeak2.buildbin-libdir && mkdir exomePeak2.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=exomePeak2.buildbin-libdir exomePeak2_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL exomePeak2_1.4.2.zip && rm exomePeak2_1.4.2.tar.gz exomePeak2_1.4.2.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
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
 43 2229k   43  980k    0     0   549k      0  0:00:04  0:00:01  0:00:03  549k
100 2229k  100 2229k    0     0   970k      0  0:00:02  0:00:02 --:--:--  971k

install for i386

* installing *source* package 'exomePeak2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'exomePeak2'
    finding HTML links ... done
    GC_content_over_grl                     html  
    GCsizeFactors-methods                   html  
    GLM_inference                           html  
    LibraryType-methods                     html  
    MeripBamFileList-class                  html  
    finding level-2 HTML links ... done

    Parameter-methods                       html  
    Results-methods                         html  
    SummarizedExomePeak-class               html  
    call_peaks_with_GLM                     html  
    convertTxDb                             html  
    ctest                                   html  
    decision_deseq2                         html  
    disj_background                         html  
    estimateSeqDepth-methods                html  
    exomePeak2                              html  
    exomePeak2Results-methods               html  
    exomePeakCalling-methods                html  
    exome_bins_from_txdb                    html  
    exonPlot                                html  
    exons_by_unique_gene                    html  
    exportResults-methods                   html  
    flank_on_exons                          html  
    glmDM-methods                           html  
    glmM-methods                            html  
    mclust_bg                               html  
    normalizeGC-methods                     html  
    plotExonLength-methods                  html  
    plotLfcGC-methods                       html  
    plotReadsGC-methods                     html  
    plotSizeFactors-methods                 html  
    quiet                                   html  
    reads_five_POS                          html  
    reads_five_POS_rev                      html  
    reduce_peaks                            html  
    remove_introns                          html  
    replace_bg                              html  
    scanMeripBAM                            html  
    sort_sep                                html  
    split_by_name                           html  
** 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

install for x64

* installing *source* package 'exomePeak2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'exomePeak2' as exomePeak2_1.4.2.zip
* DONE (exomePeak2)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'exomePeak2' successfully unpacked and MD5 sums checked

Tests output


Example timings

exomePeak2.Rcheck/examples_i386/exomePeak2-Ex.timings

nameusersystemelapsed
GCsizeFactors-methods0.050.000.05
LibraryType-methods0.230.000.23
MeripBamFileList-class0.230.000.23
Parameter-methods0.090.080.17
Results-methods1.630.121.75
SummarizedExomePeak-class26.20 1.9628.82
estimateSeqDepth-methods0.130.000.12
exomePeak281.67 0.2983.14
exomePeak2Results-methods000
exomePeakCalling-methods42.69 0.1743.20
exportResults-methods1.100.001.09
glmDM-methods5.340.005.46
glmM-methods5.220.005.22
normalizeGC-methods0.110.000.11
plotExonLength-methods0.830.000.83
plotLfcGC-methods0.190.000.19
plotReadsGC-methods0.970.000.97
plotSizeFactors-methods0.340.000.34
scanMeripBAM0.20.00.2

exomePeak2.Rcheck/examples_x64/exomePeak2-Ex.timings

nameusersystemelapsed
GCsizeFactors-methods0.050.000.04
LibraryType-methods0.190.020.21
MeripBamFileList-class0.220.010.24
Parameter-methods0.090.000.10
Results-methods0.950.020.97
SummarizedExomePeak-class27.84 1.0328.88
estimateSeqDepth-methods0.130.000.12
exomePeak278.28 0.1278.42
exomePeak2Results-methods000
exomePeakCalling-methods46.42 0.1146.54
exportResults-methods1.330.001.32
glmDM-methods5.470.005.47
glmM-methods5.360.025.38
normalizeGC-methods0.120.000.12
plotExonLength-methods0.910.000.91
plotLfcGC-methods0.180.000.18
plotReadsGC-methods1.010.001.01
plotSizeFactors-methods0.390.000.39
scanMeripBAM0.270.000.27