R Observatory: Metrics for strollur version 0.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

strollur

0.1.4Package record

Store and Transfer Amplicon Sequence Data

1packages dependsuggested by 1

1.7Kdownloads / year

91.2%test coverage

11/13flavors OK

Overview

About

Maintained by Pat SchlossCRAN page ↗GitHub ↗Website ↗Issues ↗

Stores the data associated with your amplicon sequence analysis. This includes nucleotide sequences, abundance, sample and treatment assignments, taxonomic classifications, asv, otu and phylotype clusters, metadata, trees and various reports. It is designed to facilitate data analysis across multiple R packages with utility functions to read / write from 'mothur', 'qiime2', 'dada2', and 'phyloseq'.

Changes in 0.1.4

New Features:

Expands built in read / write functions.
strollur::read_fastq() returns data.frame with fastq data.
strollur::write_fastq() writes fastq data to file.
strollur::read_quality() returns data.frame with sequence quality data.
strollur::write_quality() writes sequence quality data to file.
strollur::read_biom() returns a strollur_object.
strollur::write_biom() writes biom files containing the strollur_object.
Expands member functions of the strollur_object.
strollur_object$alignment_length() returns the sequences alignment length or -1 if the sequences are unaligned.
strollur_object$has_bin_taxonomy() returns TRUE if your dataset includes bin classifications.
strollur_object$has_sequence_taxonomy() returns TRUE if your dataset includes sequence classifications.

Show all changes in 0.1.4Hide the rest of the changes in 0.1.4

strollur_object$rename() rename the strollur object.

Enhancements:

Adds fastq, quality, sequence_tree, sample_tree, sample_distance types to:
strollur::report()
strollur_object$report()
Adds fastq type to:
strollur::add()
strollur_object$add()
Adds quality and sample_distance type to:
strollur::assign()
strollur_object$assign()

Functions for Package developers

Adds strollur::xdev_add_sequence_fastq_scores() function.
Adds strollur::xdev_alignment_length() function
Adds strollur::xdev_assign_bin_taxonomy_tidy() function.
Adds strollur::xdev_assign_sample_distances() function.
Adds strollur::xdev_assign_sequence_quality_scores function.
Adds strollur::xdev_has_bin_taxonomy() function.
Adds strollur::xdev_get_sample_distances() function.
Adds strollur::xdev_get_sequence_indexes_by_sample() function.

Bug Fixes:

strollur::summary() will now display results that accurately represent the data.

Deprecated:

Simplifies member functions of the strollur_object.
Removes strollur_object$add_sequence_tree() : Functionality now included instrollur_object$add().
Removes strollur_object$add_sample_tree() : Functionality now included instrollur_object$add().
Removes strollur_object$get_sequence_tree() : Functionality now included instrollur_object$report().
Removes strollur_object$get_sample_tree() : Functionality now included instrollur_object$report().

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("strollur", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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

Development version from mothur/strollur. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-strollur

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-strollur

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-strollur

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2ERROR11OK

Check messages

ERRORexamplesr-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

r-devel-linux-x86_64-debian-gcc

Running examples in ‘strollur-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_biom
> ### Title: Create a strollur object from a biom formatted file.
> ### Aliases: read_biom
> 
> ### ** Examples
> 
> 
> if (requireNamespace("h5lite", quietly = TRUE)) {
+   data <- strollur::read_biom(biom = strollur_example("miseq_sop.otu.biom"))
+   data
+ } else {
+   message(paste(
+     "To use this functionality you have to install the",
+     "h5lite package."
+   ))
+ }
HDF5-DIAG: Error detected in HDF5 (2.2.0) thread 1:
  #000: src/H5F.c line 575 in H5Fopen(): unable to synchronously open file
    major: File accessibility
    minor: Unable to open file
  #001: src/H5F.c line 555 in H5F__open_api_common(): unable to open file
    major: File accessibility
    minor: Unable to open file
  #002: src/H5VLcallback.c line 2803 in H5VL_file_open(): open failed
    major: Virtual Object Layer
    minor: Can't open object
  #00
...[truncated]...

  #004: src/H5VLnative_file.c line 69 in H5VL__native_file_open(): unable to open file
    major: File accessibility
    minor: Unable to open file
  #005: src/H5Fint.c line 1439 in H5F_open(): can't try opening file
    major: File accessibility
    minor: Unable to open file
  #006: src/H5FD.c line 629 in H5FD_open(): can't open file
    major: Virtual File Layer
    minor: Unable to open file
  #007: src/H5FDsec2.c line 199 in H5FD__sec2_open(): unable to open file: name = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/strollur/extdata/miseq_sop.otu.biom', errno = 30, error message = 'Read-only file system', flags = 1, o_flags = 2
    major: File accessibility
    minor: Unable to open file
Error in h5_create_group(file = file, name = "/") : 
  Failed to open or create file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/strollur/extdata/miseq_sop.otu.biom
Calls: <Anonymous> ... read_biom_hdf5 -> <Anonymous> -> h5_create_file -> h5_create_group
Execution halted

r-patched-linux-x86_64

Running examples in ‘strollur-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_biom
> ### Title: Create a strollur object from a biom formatted file.
> ### Aliases: read_biom
> 
> ### ** Examples
> 
> 
> if (requireNamespace("h5lite", quietly = TRUE)) {
+   data <- strollur::read_biom(biom = strollur_example("miseq_sop.otu.biom"))
+   data
+ } else {
+   message(paste(
+     "To use this functionality you have to install the",
+     "h5lite package."
+   ))
+ }
HDF5-DIAG: Error detected in HDF5 (2.2.0) thread 1:
  #000: src/H5F.c line 575 in H5Fopen(): unable to synchronously open file
    major: File accessibility
    minor: Unable to open file
  #001: src/H5F.c line 555 in H5F__open_api_common(): unable to open file
    major: File accessibility
    minor: Unable to open file
  #002: src/H5VLcallback.c line 2803 in H5VL_file_open(): open failed
    major: Virtual Object Layer
    minor: Can't open object
  #00
...[truncated]...
004: src/H5VLnative_file.c line 69 in H5VL__native_file_open(): unable to open file
    major: File accessibility
    minor: Unable to open file
  #005: src/H5Fint.c line 1439 in H5F_open(): can't try opening file
    major: File accessibility
    minor: Unable to open file
  #006: src/H5FD.c line 629 in H5FD_open(): can't open file
    major: Virtual File Layer
    minor: Unable to open file
  #007: src/H5FDsec2.c line 199 in H5FD__sec2_open(): unable to open file: name = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/strollur/extdata/miseq_sop.otu.biom', errno = 30, error message = 'Read-only file system', flags = 1, o_flags = 2
    major: File accessibility
    minor: Unable to open file
Error in h5_create_group(file = file, name = "/") : 
  Failed to open or create file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/strollur/extdata/miseq_sop.otu.biom
Calls: <Anonymous> ... read_biom_hdf5 -> <Anonymous> -> h5_create_file -> h5_create_group
Execution halted

ERRORtestsr-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

r-devel-linux-x86_64-debian-gcc

Running ‘testthat.R’ [82s/109s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(strollur)
  
  Attaching package: 'strollur'
  
  The following objects are masked from 'package:base':
  
      assign, names, summary
  
  > 
  > test_check("strollur")
  
  bins is not a valid type for the abundance function. Types include: 'bin', 'sequence', sample' and 'treatment'.
  Added 3 sequences.
  Added 2425 sequences.
  Added 2 resource references.
  Added 5 sequences.
  > Your tree does not contain a node for every sequence in your dataset, ignoring tree. Missing tree nodes for: seq
...[truncated]...
s distances.
  Added 1 resource references.
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 1827 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-r6_strollur.R:3:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-read_biom.R:7:3'): read_biom ───────────────────────────────────
  Error in `h5_create_group(file = file, name = "/")`: Failed to open or create file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/strollur/extdata/miseq_sop.otu.biom
  Backtrace:
      ▆
   1. └─strollur::read_biom(biom = strollur_example("miseq_sop.otu.biom")) at test-read_biom.R:7:3
   2.   └─rbiom::read_biom(biom)
   3.     └─rbiom:::read_biom_hdf5(fp)
   4.       └─h5lite::h5_open(file = fp)
   5.         └─h5lite::h5_create_file(file)
   6.           └─h5lite::h5_create_group(file = file, name = "/")
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 1827 ]
  Error:
  ! Test failures.
  Execution halted

r-patched-linux-x86_64

Running ‘testthat.R’ [121s/179s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(strollur)
  
  Attaching package: 'strollur'
  
  The following objects are masked from 'package:base':
  
      assign, names, summary
  
  > 
  > test_check("strollur")
  
  bins is not a valid type for the abundance function. Types include: 'bin', 'sequence', sample' and 'treatment'.
  Added 3 sequences.
  Added 2425 sequences.
  Added 2 resource references.
  Added 5 sequences.
  > Your tree does not contain a node for every sequence in your dataset, ignoring tree. Missing tree nodes for: se
...[truncated]...
distances.
  Added 1 resource references.
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 1827 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-r6_strollur.R:3:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-read_biom.R:7:3'): read_biom ───────────────────────────────────
  Error in `h5_create_group(file = file, name = "/")`: Failed to open or create file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/strollur/extdata/miseq_sop.otu.biom
  Backtrace:
      ▆
   1. └─strollur::read_biom(biom = strollur_example("miseq_sop.otu.biom")) at test-read_biom.R:7:3
   2.   └─rbiom::read_biom(biom)
   3.     └─rbiom:::read_biom_hdf5(fp)
   4.       └─h5lite::h5_open(file = fp)
   5.         └─h5lite::h5_create_file(file)
   6.           └─h5lite::h5_create_group(file = file, name = "/")
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 1827 ]
  Error:
  ! Test failures.
  Execution halted

CRAN check page ↗

Slowest check: 43.7 min · r-devel-windows-x86_64

Status changes

ERROR11 OK, 2 ERRORNow
ERROR12 OK, 1 ERROR2026-10-21
OK13 OK2026-10-09
ERROR12 OK, 1 ERROR2026-10-08
OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01

Show 1 earlier changeHide 1 earlier change

OK6 OK2026-06-25

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.4

READMEYes · 302 wordsVignettesYes · 9 · dynamicNEWSYes · 100% structured · mentions 0.1.4Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 98 (2 internal)includes a package overview page
Examples that run: 100%95 run in a plain check (3 of them under a condition)
Exported functions with examples: 100%
Documented parameters: 88%
Return-value docs: 99%
Help pages citing references: 6%

Vignettes (9)

Getting Started HTML
Accessing Data HTML
Data Transfers HTML
Example Analysis Across Software Tools HTML
Functions for package developers HTML
General Importing HTML
Importing from mothur HTML
Importing from phyloseq HTML
Importing from qiime2 HTML

How these are measured

Downloads

1.7K

CRAN downloads in the past year

Rank #7,974 · ~5/day · ~141/mo

Releases R versions

Daily download trend is not available in this view yet.

46830 days

1.1K90 days

1.7K1 year

Compare downloads with other packages →

Also on94 r2u1 autocran

How downloads are counted

Repository

mothur/strollur ↗Organization: mothur

0Stars

0Forks

8Open issues

0Open PRs

2Releases

432Commits

2Commit identities

amplicon-sequencingasvotusphylogenetic-analysis

License file reads as GPL-3.0 · 432 commits · Last activity 2026-10-16

Responsiveness

How these are sampled

PRs merged (all time): 82%
Median days to close, 50 most recently updated closed issues: 21
Median days to close, 50 most recently updated closed PRs: 0

Releases over time

2026-07-07 · 02026-10-21 · 2

How these are measured

PracticesBeta

14 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/mothur/strollur on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (2)

Code of conductIssue templates

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-21 · The repository has a site deploy workflow

pkgdown site last built 2026-10-21

Coverage (1)

Coverage reporting

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (4)

lintrLint workflowVS CodeRStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Installing strollur adds 81 packages (42 with compiled code, 64 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.2.0

Imports (15)

Rcpp climethodsmicroseq R.utils R6 waldo readr ape dplyr tidyr yaml rbiomstatsutils

LinkingTo (3)

Rcpp cli Rcereal

Suggests (10)

knitr rmarkdown testthat xml2 phyloseq ggplot2 phylotypr rhdf5 h5lite pak

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Depends 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

rchime

Suggests, most downloaded first

phylotypr

How these are counted

Code & Tests

Datasets

People & History

People (3)

Pat Schloss

Gregory Johnson

Author

Sarah Westcott

Author

Releases (3)

Pick two releases to compare their code metrics.

0.1.4Latest
record
2026-10-19 · current release · diff ↗ ·
added 16 exports
read_biom, read_fastq, read_quality, write_biom, write_fastq, write_quality, xdev_add_sequence_fastq_scores, xdev_assign_bin_taxonomy_tidy, xdev_assign_sample_distances, xdev_assign_sequence_quality_scores, xdev_get_alignment_length, xdev_get_bin_abundances_by_sample, xdev_get_sample_distances, xdev_get_sequence_abundances_by_sample, xdev_get_sequence_indexes_by_sample, xdev_has_bin_taxonomy
·
3 days in CRAN's queue
Listed in CRAN's incoming queue from 2026-10-16 20:20 to 2026-10-19 11:41 UTC, in 19 readings.
0.1.3
record
2026-06-24 · diff ↗ ·
added 1 export
read_mothur_oligos
0.1.2
record
2026-06-24
R
R 4.6.0 released · 2026-04-24

Across CRAN, the median accepted release of the past year spent 23 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2026-06-24
Total releases: 3 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.2.0
Download size: 3.8 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("strollur")

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

It points to 10.1128/mra.00839-26.

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 strollur version 0.1.4 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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