R Observatory: Metrics for flowr version 0.9.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2024-11-07. Its history is shown below.

Reason: requires archived package 'params'

Details below reflect version 0.9.11, its last release before removal.

flowr

0.9.11Package record

Streamlining Design and Deployment of Complex Workflows

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Sahil SethCRAN page ↗GitHub ↗

This framework allows you to design and implement complex pipelines, and deploy them on your institution's computing cluster. This has been built keeping in mind the needs of bioinformatics workflows. However, it is easily extendable to any field where a series of steps (shell commands) are to be executed in a (work)flow.

Changes in 0.9.11

> 2021-03-01

added ability to toml files
bugfix in for moab and sge schedulers (see #74 for details)
bugfix in SBATCH params
bugfix #91
add ability to parse LSF resource output
Several other bug fixes: from @sbamin fix #73, #74, #83

From NEWS.md in the release

Install

R (source archive)pak (dev)

url <- "https://cran.r-project.org/src/contrib/Archive/flowr/flowr_0.9.11.tar.gz"
pkgFile <- "flowr_0.9.11.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.9.11) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("flow-r/flowr")

Development version from flow-r/flowr. Installs pak first if it is not already available.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.9.11

READMEYes · 559 wordsVignettesYes · 3 · dynamicNEWSYes · 67% structured · mentions 0.9.11Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 34 (6 internal)
Examples that run: 45%10 run in a plain check · 12 never run
Exported functions with examples: 67%
Documented parameters: 98%
Return-value docs: 7%
Help pages citing references: 0%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on50 r2u5 autocran1.3K conda_forge483 bioconda148 c2d4u

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (4)

R >= 3.3methodsparamsutils

Imports (4)

diagram whiskertoolsreadr

LinkingTo (0)

none

Suggests (5)

reshape2 knitr testthat funr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Sahil Seth

Author, Maintainer since 0.9.6.5 (2015)

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2024-11-07
requires archived package 'params'
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.9.11
record
2021-03-02 · diff ↗ ·
added 4 exports
get_resources, get_resources_lsf, run_pipe_v2, to_df.status
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.9.10
record
2016-04-19 · diff ↗
0.9.9.5
record
2015-12-03 · diff ↗
0.9.8.2
record
2015-10-03 · diff ↗ ·
removed 2 exports
cmds_to_flow, parse_jobids

added 2 exports
is.flow, submit_run
0.9.7.10
record
2015-08-22 · diff ↗ ·
added 1 export
check_args

Show 5 earlier eventsHide 5 earlier events

0.9.7.5
record
2015-08-15 · diff ↗ ·
removed 6 exports
generate_flow_code, get_flow_status, get_resources, kill_flow, rerun_flow, submit_job

added 28 exports
as.flowdef, as.flowmat, check, fetch, fetch_conf, fetch_pipes, flowopts, get_opts, get_status, get_wds, is.flowdef, is.flowmat, kill, load_opts, opts_flow, parse_jobids, plot_flow, rerun, run, run_pipe, set_opts, setup, submit_flow, to_flow, to_flowdef, to_flowdet, to_flowmat, whisker_render
archivedRemoved from CRAN
2015-05-18
violated the CRAN policy on the use of the user's file space
R
R 3.2.0 released · 2015-04-16
0.9.6.5
record
2015-03-27
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2015-03-27
Total releases: 7 / 11 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.3

Cite

Cite this package

Run in R for the authors' entry:

citation("flowr")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1101/029710.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for flowr version 0.9.11 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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