Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:18 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 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
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 614/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
exomePeak2 1.6.1  (landing page)
Zhen Wei
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/exomePeak2
git_branch: RELEASE_3_14
git_last_commit: 6269c12
git_last_commit_date: 2021-12-10 02:57:09 -0500 (Fri, 10 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: exomePeak2
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomePeak2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings exomePeak2_1.6.1.tar.gz
StartedAt: 2022-01-20 19:37:05 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:48:50 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 705.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: exomePeak2.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomePeak2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings exomePeak2_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/exomePeak2.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.6.1'
* 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
Results,SummarizedExomePeak: no visible global function definition for
  'glm_M'
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 metadata
  samples size_factors value
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'exomePeakCalling-methods':
exomePeakCalling
  Code: function(merip_bams = NULL, txdb = NULL, bsgenome = NULL,
                 genome = NA, mod_annot = NULL, glm_type = c("DESeq2",
                 "NB", "Poisson"), background_method =
                 c("Gaussian_mixture", "m6Aseq_prior", "manual",
                 "all"), manual_background = NULL, correct_GC_bg =
                 TRUE, qtnorm = FALSE, gff_dir = NULL, fragment_length
                 = 100, binding_length = 25, step_length =
                 binding_length, min_peak_width = fragment_length/2,
                 max_peak_width = fragment_length * 100,
                 pc_count_cutoff = 5, bg_count_cutoff = 50, p_cutoff =
                 1e-05, p_adj_cutoff = NULL, log2FC_cutoff = 0,
                 parallel = 3, bp_param = NULL)
  Docs: function(merip_bams = NULL, txdb = NULL, bsgenome = NULL,
                 genome = NA, mod_annot = NULL, glm_type = c("DESeq2",
                 "NB", "Poisson"), background_method = c("all",
                 "Gaussian_mixture", "m6Aseq_prior", "manual"),
                 manual_background = NULL, correct_GC_bg = TRUE, qtnorm
                 = FALSE, gff_dir = NULL, fragment_length = 100,
                 binding_length = 25, step_length = binding_length,
                 min_peak_width = fragment_length/2, max_peak_width =
                 fragment_length * 100, pc_count_cutoff = 5,
                 bg_count_cutoff = 50, p_cutoff = 1e-05, p_adj_cutoff =
                 NULL, log2FC_cutoff = 0, parallel = 3, bp_param =
                 NULL)
  Mismatches in argument default values:
    Name: 'background_method' Code: c("Gaussian_mixture", "m6Aseq_prior", "manual", "all") Docs: c("all", "Gaussian_mixture", "m6Aseq_prior", "manual")

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'exomePeakCalling-methods'
  'max_peak_width'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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                70.35   0.36   71.63
exomePeakCalling-methods  38.35   0.13   38.65
SummarizedExomePeak-class 25.12   1.32   27.44
glmM-methods               5.14   0.00    5.14
glmDM-methods              5.09   0.00    5.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
exomePeak2                73.27   0.15   73.42
exomePeakCalling-methods  43.14   0.16   43.30
SummarizedExomePeak-class 26.32   0.93   27.25
glmDM-methods              6.99   0.01    7.00
glmM-methods               5.96   0.02    5.98
* 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: 2 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/exomePeak2.Rcheck/00check.log'
for details.



Installation output

exomePeak2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/exomePeak2_1.6.1.tar.gz && rm -rf exomePeak2.buildbin-libdir && mkdir exomePeak2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=exomePeak2.buildbin-libdir exomePeak2_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL exomePeak2_1.6.1.zip && rm exomePeak2_1.6.1.tar.gz exomePeak2_1.6.1.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
100 2188k  100 2188k    0     0  3496k      0 --:--:-- --:--:-- --:--:-- 3501k

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_1.6.1.zip
* DONE (exomePeak2)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'exomePeak2' successfully unpacked and MD5 sums checked

Tests output


Example timings

exomePeak2.Rcheck/examples_i386/exomePeak2-Ex.timings

nameusersystemelapsed
GCsizeFactors-methods0.070.000.07
LibraryType-methods0.190.000.19
MeripBamFileList-class0.310.000.31
Parameter-methods0.160.000.16
Results-methods1.330.311.64
SummarizedExomePeak-class25.12 1.3227.44
estimateSeqDepth-methods0.110.000.11
exomePeak270.35 0.3671.63
exomePeak2Results-methods000
exomePeakCalling-methods38.35 0.1338.65
exportResults-methods1.040.011.05
glmDM-methods5.090.005.11
glmM-methods5.140.005.14
normalizeGC-methods0.110.000.11
plotExonLength-methods0.840.020.86
plotLfcGC-methods0.160.000.16
plotReadsGC-methods0.890.000.89
plotSizeFactors-methods0.370.000.38
scanMeripBAM0.190.000.18

exomePeak2.Rcheck/examples_x64/exomePeak2-Ex.timings

nameusersystemelapsed
GCsizeFactors-methods0.040.000.05
LibraryType-methods0.340.020.36
MeripBamFileList-class0.260.000.26
Parameter-methods0.110.000.11
Results-methods1.820.001.81
SummarizedExomePeak-class26.32 0.9327.25
estimateSeqDepth-methods0.120.000.12
exomePeak273.27 0.1573.42
exomePeak2Results-methods000
exomePeakCalling-methods43.14 0.1643.30
exportResults-methods1.480.001.48
glmDM-methods6.990.017.00
glmM-methods5.960.025.98
normalizeGC-methods0.130.000.13
plotExonLength-methods101
plotLfcGC-methods0.220.000.22
plotReadsGC-methods101
plotSizeFactors-methods0.50.00.5
scanMeripBAM0.360.000.36