Mahmoud Ahmed
| Snapshot Date: 2022-03-16 13:55:23 -0400 (Wed, 16 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/segmenter |
| git_branch: master |
| git_last_commit: 2d0a73d |
| git_last_commit_date: 2021-10-26 13:10:57 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-17 11:08:50 -0400 (Thu, 17 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" | 4060 |
| 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 segmenter package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/segmenter.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 1762/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| segmenter 1.1.0 (landing page) Mahmoud Ahmed
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: segmenter |
| Version: 1.1.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:segmenter.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings segmenter_1.1.0.tar.gz |
| StartedAt: 2022-03-16 20:09:06 -0400 (Wed, 16 Mar 2022) |
| EndedAt: 2022-03-16 20:16:14 -0400 (Wed, 16 Mar 2022) |
| EllapsedTime: 427.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: segmenter.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:segmenter.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings segmenter_1.1.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/segmenter.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 'segmenter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmenter' version '1.1.0'
* 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 whether package 'segmenter' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
java 3.8Mb
* 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotate_segments 23.23 1.86 34.40
learn_model 0.14 0.03 14.25
binarize_bam 0.00 0.02 9.95
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/segmenter.Rcheck/00check.log'
for details.
segmenter.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL segmenter
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'segmenter' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'segmenter'
finding HTML links ... done
accessors html
annotate_segments html
binarize_bam html
binarize_bed html
compare_models html
count_reads_ranges html
dot-Binarize html
dot-LearnModel html
emissions_file html
enrichment_files html
get_frequency html
get_width html
learn_model html
merge_segments_bins html
methods html
model_file html
overlap_files html
plot_heatmap html
range_bins html
range_counts html
read_bam_file html
read_bins_file html
read_cellmark_file html
read_chromsize_file html
read_emissions_file html
read_enrichment_file html
read_model_file html
read_overlap_file html
read_segements_file html
read_transitions_file html
segmentation html
segments_files html
test_obj html
test_objs html
tidy_ranges html
transitions_file 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 (segmenter)
Making 'packages.html' ... done
segmenter.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(segmenter)
>
> test_check("segmenter")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 123 ]
>
> proc.time()
user system elapsed
43.42 6.35 126.14
segmenter.Rcheck/segmenter-Ex.timings
| name | user | system | elapsed | |
| accessors | 0.11 | 0.00 | 0.14 | |
| annotate_segments | 23.23 | 1.86 | 34.40 | |
| binarize_bam | 0.00 | 0.02 | 9.95 | |
| compare_models | 0.00 | 0.00 | 0.03 | |
| emissions_file | 0 | 0 | 0 | |
| enrichment_files | 0 | 0 | 0 | |
| get_frequency | 0.03 | 0.00 | 0.05 | |
| get_width | 0.45 | 0.25 | 1.39 | |
| learn_model | 0.14 | 0.03 | 14.25 | |
| methods | 0 | 0 | 0 | |
| model_file | 0 | 0 | 0 | |
| overlap_files | 0 | 0 | 0 | |
| plot_heatmap | 0.41 | 0.05 | 0.45 | |
| read_bam_file | 0.02 | 0.00 | 0.02 | |
| read_bins_file | 2.48 | 0.43 | 2.92 | |
| read_cellmark_file | 0 | 0 | 0 | |
| read_chromsize_file | 0.00 | 0.02 | 0.01 | |
| read_emissions_file | 0 | 0 | 0 | |
| read_enrichment_file | 0 | 0 | 0 | |
| read_model_file | 0 | 0 | 0 | |
| read_overlap_file | 0 | 0 | 0 | |
| read_segements_file | 0.03 | 0.00 | 0.04 | |
| read_transitions_file | 0 | 0 | 0 | |
| segments_files | 0 | 0 | 0 | |
| tidy_ranges | 0.02 | 0.02 | 0.03 | |
| transitions_file | 0 | 0 | 0 | |