Comments (10)
I don't know if you already solved this issue, but you likely have openbabel installed in a different directory. Try opening your terminal and typing where obabel
,
then you can trace down the library it is looking for and symlink it into the directory where R is expecting to find it.
For me, I installed openbabel with miniconda, so I found it in my miniconda packages.
Then you can use something like the following line to create the symlink:
sudo ln -s ~/opt/miniconda3/pkgs/openbabel-3.1.1-py39hb4f85b1_3 /usr/local/opt/open-babel
from mspcompiler.
I get the following error:
The downloaded binary packages are in
/var/folders/j7/338rf36x105g2zk_2q6wmw600000gn/T//RtmpC2cfp6/downloaded_packages
✓ checking for file ‘/private/var/folders/j7/338rf36x105g2zk_2q6wmw600000gn/T/RtmpC2cfp6/remotes10ee3d7b7c08/QizhiSu-mspcompiler-703f515/DESCRIPTION’ (343ms)
─ preparing ‘mspcompiler’:
✓ checking DESCRIPTION meta-information ...
─ installing the package to build vignettes (379ms)
-----------------------------------
─ installing *source* package ‘mspcompiler’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: .onLoad failed in loadNamespace() for 'ChemmineOB', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/ChemmineOB/libs/ChemmineOB.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/ChemmineOB/libs/ChemmineOB.so, 10): Library not loaded: /usr/local/opt/open-babel/lib/libopenbabel.7.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/ChemmineOB/libs/ChemmineOB.so
Reason: image not found
Execution halted
ERROR: lazy loading failed for package ‘mspcompiler’
─ removing ‘/private/var/folders/j7/338rf36x105g2zk_2q6wmw600000gn/T/RtmpN7E44i/Rinst10fbe64f4d67f/mspcompiler’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'mspcompiler' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> call: dyn.load(file, DLLpath = DLLpath, ...)
E> error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/ChemmineOB/libs/ChemmineOB.so':
E> dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/ChemmineOB/libs/ChemmineOB.so, 10): Library not loaded: /usr/local/opt/open-babel/lib/libopenbabel.7.dylib
E> Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/ChemmineOB/libs/ChemmineOB.so
E> Reason: image not found
E> Execution halted
E> ERROR: lazy loading failed for package ‘mspcompiler’
E> * removing ‘/private/var/folders/j7/338rf36x105g2zk_2q6wmw600000gn/T/RtmpN7E44i/Rinst10fbe64f4d67f/mspcompiler’
E> -----------------------------------
E> ERROR: package installation failed
from mspcompiler.
Hi,
Did you try to install ChemmineR and ChemmineOB first following the code in the readme?
from mspcompiler.
Hi, Did you try to install ChemmineR and ChemmineOB first following the code in the readme?
Yes, I have. Once I do enter the code above, do I then re-try the installation? This is what I have been doing. When I re-try installing, I still have issues with ChemmineR and ChemmineOB - I am prompted to update, and it seems no matter which update option I try there is still problems with the installation. Thanks for your response!
See below for more details (I have labeled my entries with ###, all other lines are output):
> if (!requireNamespace("BiocManager", quietly = TRUE)) ###
+ install.packages("BiocManager") ###
>
> BiocManager::install("ChemmineR")###
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.12 (BiocManager 1.30.16), R 4.0.3 (2020-10-10)
Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to
re-install: 'ChemmineR'
>
> if (!requireNamespace("BiocManager", quietly = TRUE)) ###
+ install.packages("BiocManager") ###
>
> BiocManager::install("ChemmineOB") ###
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.12 (BiocManager 1.30.16), R 4.0.3 (2020-10-10)
Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to
re-install: 'ChemmineOB'
> install.packages("devtools") ###
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/devtools_2.4.2.tgz'
Content type 'application/x-gzip' length 393203 bytes (383 KB)
==================================================
downloaded 383 KB
The downloaded binary packages are in
/var/folders/j7/338rf36x105g2zk_2q6wmw600000gn/T//Rtmp4BxHOB/downloaded_packages
> devtools::install_github("QizhiSu/mspcompiler", build_vignettes = TRUE) ###
Downloading GitHub repo QizhiSu/mspcompiler@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: ChemmineR (3.42.2 -> 13ab93a3f...) [GitHub]
5: ChemmineOB (1.28.4 -> d4314fc44...) [GitHub]
Enter one or more numbers, or an empty line to skip updates: 1 ###
ChemmineR (3.42.2 -> 13ab93a3f...) [GitHub]
ChemmineOB (1.28.4 -> d4314fc44...) [GitHub]
Downloading GitHub repo girke-lab/ChemmineR@HEAD
Error: Failed to install 'mspcompiler' from GitHub:
Failed to install 'ChemmineR' from GitHub:
Could not find tools necessary to compile a package
Call `pkgbuild::check_build_tools(debug = TRUE)` to diagnose the problem.
from mspcompiler.
I think the problem was ChemminR and ChemmineOB. Maybe you can try to reinstall them using the force argument.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChemmineR", force = TRUE)
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChemmineOB", force = TRUE)
Thanks for your attention.
Best Qizhi Su
from mspcompiler.
I am able to reinstall them using the force argument as shown in the code above. I then use the code:
install.packages("devtools")
devtools::install_github("QizhiSu/mspcompiler", build_vignettes = TRUE)
This immediately prompts me to update as shown in the image below. I have also tried entering in all of the numbers that it suggests.
Besides entering in numbers to update, I can also restart R to update as shown in the pic below.
How should I proceed from the point shown in the image below?
I am able to successfully install ChemmineR and ChemmineOB using the code from your previously reply. It says they are successfully installed, but when I then try to install mspcompiler, it seems no matter which option I choose for updating that building the vignette fails. Do I need to load a specific library before trying to install mspcompiler?
from mspcompiler.
Hi,
No specific library is required before installation. It seems that you still have problem with ChemmineR and ChemmineOB. I reconfirmed that it can be successfully installed on my side and my friend's computer. What operating system are you using?
Maybe you can take a look in the following links:
https://support.bioconductor.org/p/119886/
girke-lab/ChemmineOB#11
Hope it will be helpful.
Best regards
from mspcompiler.
Hi, I have solved the problem! Thank you for your help in doing so.
from mspcompiler.
@tlgroff Hi could you please tell me what was the problem?
from mspcompiler.
I met the same issue but on Windows 10. I think it might be caused by Patroon package which installed open babel automatically on my PC. I uninstalled open babel, then installed it again, and the problem solved.
from mspcompiler.
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from mspcompiler.