Why does bio3d no longer support EDDM and cannot download and install it despite trying various methods

[Jianlin Li]

devtools::install_bitbucket("Grantlab/bio3d-eddm")
Downloading bitbucket repo Grantlab/bio3d-eddm@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
cannot open URL 'https://bitbucket.org/Grantlab/bio3d-eddm/get/HEAD.tar.gz'

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install.packages("bio3d-eddm")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Warning message:
package ‘bio3d-eddm’ is not available for this version of R

A version of this package 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

The R version we are using is 4.4.1, running on the Ubuntu 18.04 system, the Bio3D version we are using is 2.4-4.

Please tell me how to solve the problem.

[Xinqiu Yao]

You need to install ‘bio3d.core’ first. Here is the instruction:

devtools::install_bitbucket("Grantlab/bio3d/bio3d-core", ref="core")
devtools::install_bitbucket("Grantlab/bio3d-eddm")

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[Jianlin Li]

devtools::install_bitbucket("Grantlab/bio3d/bio3d-core", ref="core")
Downloading bitbucket repo Grantlab/bio3d@core
Error in utils::download.file(url, path, method = method, quiet = quiet, :
cannot open URL 'https://bitbucket.org/Grantlab/bio3d/get/core.tar.gz'

Sorry, look at this error, it prompts that the URL cannot be opened, I guess that's why EDDM can't download and install it. In fact, when installing bio3d and related content through devtools, the URL shows that it cannot be opened, which may require your confirmation.

[Xinqiu Yao]

Hi,

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I can install it successfully using the above command. I have tested it in different versions of Ubuntu and R and have no problems. Please contact your administrator and check if it is related to your system setup.

> devtools::install_bitbucket("Grantlab/bio3d/bio3d-core", ref="core")
Downloading bitbucket repo Grantlab/bio3d@core
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/Rtmp9O3Ykf/remotesd182ca4776f/Grantlab-bio3d-144f93357a24/bio3d-core/DESCRIPTION’ ...
─  preparing ‘bio3d.core’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘bio3d.core_2.5-0.9000.tar.gz’

… (output cut)

** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bio3d.core)

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[Jianlin Li]

Thank you very much! I have solved this problem done!