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This page was generated on 2021-12-03 13:05:46 -0500 (Fri, 03 Dec 2021).

CHECK results for exomePeak2 on machv2

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 1.6.0  (landing page)
Zhen Wei
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/exomePeak2
git_branch: RELEASE_3_14
git_last_commit: 50ec4d5
git_last_commit_date: 2021-10-26 12:57:41 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:exomePeak2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings exomePeak2_1.6.0.tar.gz
StartedAt: 2021-12-02 14:20:46 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 14:31:28 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 641.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: exomePeak2.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:exomePeak2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings exomePeak2_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/exomePeak2.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.6.0’
* 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
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 'exomePeak2':
exomePeak2
  Code: function(bam_ip = NULL, bam_input = NULL, bam_treated_ip =
                 NULL, bam_treated_input = NULL, txdb = NULL, bsgenome
                 = NULL, genome = NA, gff_dir = NULL, mod_annot = NULL,
                 paired_end = FALSE, library_type = c("unstranded",
                 "1st_strand", "2nd_strand"), 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 = 1,
                 background_method = c("all", "Gaussian_mixture",
                 "m6Aseq_prior", "manual"), manual_background = NULL,
                 correct_GC_bg = TRUE, qtnorm = FALSE, glm_type =
                 c("DESeq2", "Poisson", "NB"), LFC_shrinkage =
                 c("apeglm", "ashr", "Gaussian", "none"),
                 export_results = TRUE, export_format = c("CSV", "BED",
                 "RDS"), table_style = c("bed", "granges"),
                 save_plot_GC = TRUE, save_plot_analysis = FALSE,
                 save_plot_name = "", save_dir = "exomePeak2_output",
                 peak_calling_mode = c("exon", "full_tx",
                 "whole_genome"))
  Docs: function(bam_ip = NULL, bam_input = NULL, bam_treated_ip =
                 NULL, bam_treated_input = NULL, txdb = NULL, bsgenome
                 = NULL, genome = NA, gff_dir = NULL, mod_annot = NULL,
                 paired_end = FALSE, library_type = c("unstranded",
                 "1st_strand", "2nd_strand"), fragment_length = 100,
                 binding_length = 25, step_length = binding_length,
                 min_peak_width = fragment_length/2, max_peak_width =
                 fragment_length * 10, pc_count_cutoff = 5,
                 bg_count_cutoff = 50, p_cutoff = 1e-05, p_adj_cutoff =
                 NULL, log2FC_cutoff = 0, parallel = 1,
                 background_method = c("all", "Gaussian_mixture",
                 "m6Aseq_prior", "manual"), manual_background = NULL,
                 correct_GC_bg = TRUE, qtnorm = FALSE, glm_type =
                 c("DESeq2", "Poisson", "NB"), LFC_shrinkage =
                 c("apeglm", "ashr", "Gaussian", "none"),
                 export_results = TRUE, export_format = c("CSV", "BED",
                 "RDS"), table_style = c("bed", "granges"),
                 save_plot_GC = TRUE, save_plot_analysis = FALSE,
                 save_plot_name = "", save_dir = "exomePeak2_output",
                 peak_calling_mode = c("exon", "full_tx",
                 "whole_genome"))
  Mismatches in argument default values:
    Name: 'max_peak_width' Code: fragment_length * 100 Docs: fragment_length * 10

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("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 * 10, 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: 'max_peak_width' Code: fragment_length * 100 Docs: fragment_length * 10
\S4method{exomePeakCalling}{MeripBamFileList}
  Code: 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 = 1, 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 * 10, pc_count_cutoff = 5,
                 bg_count_cutoff = 50, p_cutoff = 1e-05, p_adj_cutoff =
                 NULL, log2FC_cutoff = 0, parallel = 1, bp_param =
                 NULL)
  Mismatches in argument default values:
    Name: 'max_peak_width' Code: fragment_length * 100 Docs: fragment_length * 10

Codoc mismatches from documentation object 'glmM-methods':
glmM
  Code: function(sep, glm_type = c("DESeq2", "NB", "Poisson"),
                 LFC_shrinkage = c("apeglm", "Gaussian", "ashr",
                 "none"), ...)
  Docs: function(sep, glm_type = c("DESeq2", "NB", "Poisson"),
                 LFC_shrinkage = c("apeglm", "Gaussian", "ashr"), ...)
  Mismatches in argument default values:
    Name: 'LFC_shrinkage' Code: c("apeglm", "Gaussian", "ashr", "none") Docs: c("apeglm", "Gaussian", "ashr")
\S4method{glmM}{SummarizedExomePeak}
  Code: function(sep, glm_type = c("DESeq2", "NB", "Poisson"),
                 LFC_shrinkage = c("apeglm", "Gaussian", "ashr",
                 "none"), ...)
  Docs: function(sep, glm_type = c("DESeq2", "NB", "Poisson"),
                 LFC_shrinkage = c("apeglm", "Gaussian", "ashr"), ...)
  Mismatches in argument default values:
    Name: 'LFC_shrinkage' Code: c("apeglm", "Gaussian", "ashr", "none") Docs: c("apeglm", "Gaussian", "ashr")

* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
exomePeak2                114.696  0.574 115.400
exomePeakCalling-methods   63.644  0.295  63.988
SummarizedExomePeak-class  37.808  0.760  38.656
glmM-methods                8.836  0.024   8.869
glmDM-methods               7.651  0.021   7.683
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/exomePeak2.Rcheck/00check.log’
for details.



Installation output

exomePeak2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL exomePeak2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-methods0.0970.0090.108
LibraryType-methods0.3800.0420.424
MeripBamFileList-class0.4320.0520.484
Parameter-methods0.1550.0190.174
Results-methods1.3470.0171.365
SummarizedExomePeak-class37.808 0.76038.656
estimateSeqDepth-methods0.1350.0010.136
exomePeak2114.696 0.574115.400
exomePeak2Results-methods0.0180.0020.019
exomePeakCalling-methods63.644 0.29563.988
exportResults-methods1.6260.0071.633
glmDM-methods7.6510.0217.683
glmM-methods8.8360.0248.869
normalizeGC-methods0.2250.0020.227
plotExonLength-methods1.4960.0091.507
plotLfcGC-methods0.2960.0020.299
plotReadsGC-methods1.6100.0121.627
plotSizeFactors-methods0.6510.0020.654
scanMeripBAM0.2930.0050.298