R Observatory: Metrics for TCGAretriever version 1.10.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TCGAretriever

1.10.3Package record

Retrieve Genomic and Clinical Data from CBioPortal Including TCGA Data

0packages depend

3.9Kdownloads / year

–test coverage

7/13flavors OK

Overview

About

Maintained by Damiano FantiniCRAN page ↗Website ↗

The Cancer Genome Atlas (TCGA) is a program aimed at improving our understanding of Cancer Biology. Several TCGA Datasets are available online. 'TCGAretriever' helps accessing and downloading TCGA data hosted on 'cBioPortal' via its Web Interface (see https://www.cbioportal.org/ for more information).

Install

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

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

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

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-tcgaretriever

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-TCGAretriever

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-TCGAretriever

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

1ERROR5NOTE7OK

Check messages

ERRORre-building of vignette outputsr-release-macos-arm64

Error(s) in re-building vignettes:
--- re-building ‘get_started_with_TCGAretriever.Rmd’ using rmarkdown
Error in .Call(R_curl_fetch_memory, enc2utf8(url), handle, nonblocking) : 
  reached elapsed time limit


Quitting from get_started_with_TCGAretriever.Rmd:47-55 [unnamed-chunk-1]
Execution halted

NOTEdependencies in R coder-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Base package in Suggests/Enhances imported in NAMESPACE:
  ‘stats’

r-devel-windows-x86_64

Base package in Suggests/Enhances imported in NAMESPACE:
  'stats'

CRAN check page ↗

Slowest check: 2.5 min · r-oldrel-macos-x86_64

Status changes

ERROR7 OK, 5 NOTE, 1 ERRORNow
ERROR11 OK, 1 ERROR2026-04-27
OK14 OK2026-03-25
ERROR12 OK, 2 ERROR2026-03-21
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.10.3

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsiteYes

Help pages: 15 (2 internal)includes a package overview page
Examples that run: 80%12 run in a plain check · 3 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 93%

Vignettes (1)

Get Started with TCGAretriever HTML

How these are measured

Downloads

3.9K

CRAN downloads in the past year

Rank #12,595 · ~11/day · ~323/mo

Releases R versions

Daily download trend is not available in this view yet.

33730 days

89690 days

3.9K1 year

Compare downloads with other packages →

Also on94 r2u3 autocran

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing TCGAretriever adds 19 packages (15 with compiled code, 19 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, openssl 1.1 MB.

Depends (1)

R >= 3.5.0

Imports (3)

httr reshape2 jsonlite

LinkingTo (0)

none

Suggests (6)

statsutilsknitr rmarkdown ggplot2 dplyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Damiano Fantini

Author, Maintainer since 1.1 (2016)

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-02-23
1.10.3Latest
record
2026-02-23 · current release · diff ↗ ·
added 1 export
check_TCGAretriever_connection
archivedRemoved from CRAN
2026-02-20
policy violation On Internet access
1.10.1
record
2025-11-20 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.9.1
record
2024-01-23 · diff ↗ ·
removed 3 exports
get_ext_mutation, get_profile_data, show_head

added 3 exports
get_gene_identifiers, get_molecular_data, get_mutation_data
1.7
record
2023-07-10 · diff ↗ ·
removed 2 exports
get_protein_data, get_protein_info

added 1 export
show_head
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
R
R 4.0.0 released · 2020-04-24
1.5
record
2019-12-17 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 12 exports
expand_cases, fetch_all_tcgadata, get_cancer_studies, get_cancer_types, get_case_lists, get_clinical_data, get_ext_mutation, get_genetic_profiles, get_profile_data, get_protein_data, get_protein_info, make_groups
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23

Show 4 earlier eventsHide 4 earlier events

R
R 3.4.0 released · 2017-04-21
1.3
record
2016-07-30 · diff ↗
1.1
record
2016-07-13
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-07-13
Total releases: 7 / 10 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 8.0 KB / 1 file
Download size: 547 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TCGAretriever")

Format

Fantini, D. (2026). TCGAretriever: Retrieve Genomic and Clinical Data from CBioPortal Including TCGA Data (Version 1.10.3) [Computer software]. https://doi.org/10.32614/CRAN.package.TCGAretriever

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 TCGAretriever version 1.10.3 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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