Zhen Wei
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/exomePeak2 |
| git_branch: master |
| git_last_commit: 5d8ded6 |
| git_last_commit_date: 2021-11-20 04:00:53 -0400 (Sat, 20 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:29 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 617/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| exomePeak2 1.7.1 (landing page) Zhen Wei
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: exomePeak2 |
| Version: 1.7.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:exomePeak2.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings exomePeak2_1.7.1.tar.gz |
| StartedAt: 2022-03-17 19:03:32 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:08:57 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 324.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: exomePeak2.Rcheck |
| Warnings: 2 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:exomePeak2.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings exomePeak2_1.7.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/exomePeak2.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.7.1'
* 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
* 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 40.85 0.53 41.42
exomePeakCalling-methods 23.89 0.14 24.07
SummarizedExomePeak-class 14.62 1.00 15.66
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/exomePeak2.Rcheck/00check.log'
for details.
exomePeak2.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL exomePeak2
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (exomePeak2)
Making 'packages.html' ... done
exomePeak2.Rcheck/exomePeak2-Ex.timings
| name | user | system | elapsed | |
| GCsizeFactors-methods | 0.03 | 0.00 | 0.03 | |
| LibraryType-methods | 0.14 | 0.00 | 0.14 | |
| MeripBamFileList-class | 0.2 | 0.0 | 0.2 | |
| Parameter-methods | 0.09 | 0.00 | 0.09 | |
| Results-methods | 0.80 | 0.02 | 0.83 | |
| SummarizedExomePeak-class | 14.62 | 1.00 | 15.66 | |
| estimateSeqDepth-methods | 0.08 | 0.00 | 0.08 | |
| exomePeak2 | 40.85 | 0.53 | 41.42 | |
| exomePeak2Results-methods | 0.01 | 0.00 | 0.01 | |
| exomePeakCalling-methods | 23.89 | 0.14 | 24.07 | |
| exportResults-methods | 0.72 | 0.00 | 0.74 | |
| glmDM-methods | 2.18 | 0.00 | 2.18 | |
| glmM-methods | 2.52 | 0.01 | 2.53 | |
| normalizeGC-methods | 0.06 | 0.00 | 0.07 | |
| plotExonLength-methods | 0.99 | 0.00 | 0.98 | |
| plotLfcGC-methods | 0.2 | 0.0 | 0.2 | |
| plotReadsGC-methods | 0.95 | 0.00 | 0.95 | |
| plotSizeFactors-methods | 0.37 | 0.00 | 0.38 | |
| scanMeripBAM | 0.14 | 0.04 | 0.17 | |