Re: [Bioc-devel] R package on Github uses Bioconductor depenencies and cant be installed.
What command was used? BiocManager::install should resolve the dependencies
whereas straight use of install.packages would not.
On Wed, Feb 28, 2024 at 9:07 AM Ruff, Sergej
wrote:
> Hello,
>
>
> I have an R package on Github that uses Bioconductor dependencies:
>
>
> https://github.com/klausjung-hannover/bootGSEA/blob/main/DESCRIPTION
>
>
> 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://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-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
>
> [[alternative HTML version deleted]]
>
> ___
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>
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Re: [Bioc-devel] R package on Github uses Bioconductor depenencies and cant be installed.
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 on behalf of Ruff, Sergej
Sent: Wednesday, February 28, 2024 8:59 AM
To: bioc-devel@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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[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://github.com/klausjung-hannover/bootGSEA/blob/main/DESCRIPTION
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://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-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
[[alternative HTML version deleted]]
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