[Bioc-devel] R package on Github uses Bioconductor depenencies and cant be installed.

[Kern, Lori]

Bioconductor packages need to be installed with BiocManager.  If you do BiocManager::install("klausjung-hannover/bootGSEA")  That should also find Bioconductor package dependencies.



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Ruff, Sergej <Sergej.Ruff using tiho-hannover.de>
Sent: Wednesday, February 28, 2024 8:59 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] R package on Github uses Bioconductor depenencies and cant be installed.

Hello,


I have an R package on  Github that uses Bioconductor dependencies:


https://secure-web.cisco.com/1mWRxOSlvd9QbWzcsR4ms_SdfUVeG_NS-4PWZehnLBuUGioIAl5-RzQtpIkRALKPMLukxikylL8LraUMueJUB_hjkYjGBv5vn2XFI16WqyL6qFglYE8sNL6Wx1diKBpC90DfA3CUP1BTgC-Mj74Ud0zf-QG42jLhkliViAaeWQzfmichedi3YXRAMaqH1uYP9OIswTrYrnlTimoU8cK6fLnjD7ogMSjw1Mc3WoExDgDPDyQV3Iptdk_1EhabzC-Y7gvtDk0QDzmNuc1MSfbER0terLnJBPqttea34jhLRTKUN1oc5tlEAF2UZPtaaBfxO/https%3A%2F%2Fgithub.com%2Fklausjung-hannover%2FbootGSEA%2Fblob%2Fmain%2FDESCRIPTION


One reviewer recently sent me a message that he can�t install the package.

Itried installing the package on a new device and got the following error:


Installing package into �/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3�
(as �lib� is unspecified)
ERROR: dependencies �topGO�, �ReactomePA�, �org.Mm.eg.db� are not available for package �bootGSEA�
* removing �/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3/bootGSEA�
Warning messages:
1: packages �org.Mm.eg.db�, �ReactomePA�, �topGO� are not available for this version of R

Versions of these packages for your version of R might be available elsewhere,
see the ideas at
https://secure-web.cisco.com/1h1CY3ac_CGJrKAEZ5jVkjq35qYN2XCsfI6LGP-42NkgSoTaRx83wf-QIHGIoBR3sVmpGJ40cqAUfYKg4kT6EFSSPmi9kyzZL7wfBaouyo8vPc_Kt-avJX6NQbTC5xiLtwnezxo7QZ_gUSX0EYm39MuNl8KU_NfvfXUK6b6HzfjtgIaK5CIGmsfQfd8s26K5DXbRR0nC2AyZJOQEok_SXHUdXxGeoT62N1f-Bx-a8Fsad8sfz2j2kxYsKeuYj7YuhHts9lk_35FzqV2ebiQhklvgwrrtEn4jpnImnI0EDtGD3dxngOUFQpp1Jpkf7ZFBK/https%3A%2F%2Fcran.r-project.org%2Fdoc%2Fmanuals%2Fr-patched%2FR-admin.html%23Installing-packages
2: In i.p(...) :
  installation of package �/tmp/Rtmpnq6hVG/filed7528253e49/bootGSEA_1.0.tar.gz� had non-zero exit status


The CRAN dependencies install fine but Bioconductor packages refuse to install.


Is there a way to solve the problem?


I use the following command:


library(devtools)
install_github("klausjung-hannover/bootGSEA")


I read that I should use biocView to the description file, but i couldn�t find a good source where someone explains why thats right or what biocView does?

Could someone help me with my problem and explain if adding Biocview helps and more importantly why?


Best, Sergej

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