Installing error in the Bio3D family
Issue #789
resolved
Hello team,
I tried to install the bio3d family packages (nma, cna, eddm) into my system. But the installation did not work well except for bio3d-eddm. Could you tell me to solve the problem?
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
bio3d 2.4-1.9000
One error was reported in installing bio3d. But bio3d seems to work well.
> library(devtools)
> install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/")
Downloading bitbucket repo Grantlab/bio3d@HEAD
Grantlab-bio3d-8b835901ded6/vignettes_devel/enma_vignettes/bio3d.bib: Can't create '\\\\?\\C:\\Users\\username~1\\AppData\\Local\\Temp\\RtmpMbHngJ\\remotes184019581fce\\Grantlab-bio3d-8b835901ded6\\vignettes_devel\\enma_vignettes\\bio3d.bib'
tar.exe: Error exit delayed from previous errors.
~
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bio3d)
警告メッセージ:
utils::untar(tarfile, ...) で:
‘tar.exe -xf "C:\Users\username~1\AppData\Local\Temp\RtmpMbHngJ\file18402e262c15.tar.gz" -C "C:/Users/username~1/AppData/Local/Temp/RtmpMbHngJ/remotes184019581fce"’ returned error code 1
one example for bio3d-cna
> devtools::install_bitbucket("Grantlab/bio3d-cna")
Downloading bitbucket repo Grantlab/bio3d-cna@HEAD
Skipping 1 packages not available: bio3d.core
√ checking for file 'C:\Users\Username\AppData\Local\Temp\RtmpodmBnb\remotes39503ef0410f\Grantlab-bio3d-cna-68f262453e8f/DESCRIPTION' (449ms)
- preparing 'bio3d.cna': (415ms)
√ checking DESCRIPTION meta-information ...
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'bio3d.cna_0.1.0.9000.tar.gz'
Installing package into ‘C:/Users/Username/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
ERROR: dependency 'bio3d.core' is not available for package 'bio3d.cna'
* removing 'C:/Users/Username/Documents/R/win-library/4.0/bio3d.cna'
エラー: Failed to install 'bio3d.cna' from Bitbucket:
(警告から変換されました) installation of package ‘C:/Users/Username/AppData/Local/Temp/RtmpodmBnb/file39503c1a6842/bio3d.cna_0.1.0.9000.tar.gz’ had non-zero exit status
Comments (3)
-
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reporter Thank you for your prompt reply.
I completed the installation without any problems.
I am deeply grateful to the team for developing this wonderful program.
-
reporter - changed status to resolved
- Log in to comment
Hi,
Try to install ‘bio3d-core’ instead of ‘bio3d’.
First, remove your currently installed version,
remove.packages(“bio3d”)
. Then, type:install_bitbucket("Grantlab/bio3d", subdir = "bio3d-core", ref="core")
Now you should be able to install bio3d-cna properly:
install_bitbucket("Grantlab/bio3d-cna")
Remember, in this new phase, the main bio3d functions will be loaded by
library(bio3d.core)
rather thanlibrary(bio3d)