Zhen Wei
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 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 -0400 (Fri, 10 Dec 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:31 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 614/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| exomePeak2 1.6.1 (landing page) Zhen Wei
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| 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: 2022-04-12 19:27:24 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 19:38:29 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 664.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: exomePeak2.Rcheck |
| Warnings: 2 |
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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
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/exomePeak2.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.6.1'
* 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 64.06 1.05 65.16
exomePeakCalling-methods 36.67 0.20 37.21
SummarizedExomePeak-class 23.75 1.53 25.52
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
exomePeak2 73.53 0.19 74.25
exomePeakCalling-methods 37.86 0.14 38.00
SummarizedExomePeak-class 22.89 1.30 24.28
glmM-methods 5.34 0.01 5.36
* 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.
exomePeak2.Rcheck/00install.out
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###
### 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
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
12 2188k 12 272k 0 0 725k 0 0:00:03 --:--:-- 0:00:03 725k
82 2188k 82 1809k 0 0 1317k 0 0:00:01 0:00:01 --:--:-- 1318k
100 2188k 100 2188k 0 0 1404k 0 0:00:01 0:00:01 --:--:-- 1404k
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
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exomePeak2.Rcheck/examples_i386/exomePeak2-Ex.timings
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exomePeak2.Rcheck/examples_x64/exomePeak2-Ex.timings
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