Comments (9)
Any suggestions?
from leafcutter.
I was able to start the installation process by using the nested folder, i.e. leafcutter/leafcutter
.
(leafcutter) [obotvinnik@tscc-login2 leafcutter]$ ls
clustering example_data leafcutter LICENSE other_ideas README.md scripts
(leafcutter) [obotvinnik@tscc-login2 leafcutter]$ R CMD INSTALL --build leafcutter
* installing to library ‘/home/obotvinnik/anaconda/envs/leafcutter/lib/R/library’
ERROR: dependencies ‘rstan’, ‘R.utils’, ‘gridExtra’, ‘Hmisc’, ‘StanHeaders’ are not available for package ‘leafcutter’
* removing ‘/home/obotvinnik/anaconda/envs/leafcutter/lib/R/library/leafcutter’
And I tried to install rstan
and friends but ran into conflicts with the base R command.
(leafcutter) [obotvinnik@tscc-login2 leafcutter]$ conda install -c mittner r-rstan
Fetching package metadata .............
Solving package specifications: ....
UnsatisfiableError: The following specifications were found to be in conflict:
- r-rstan
- r-tibble -> r-base 3.3.1*
Use "conda info <package>" to see the dependencies for each package.
I find these version-specificities of R extremely frustrating and a major point why I don't use R for my research -- I can never install anything!! To make it easier for new users, can you provide clear installation instructions, using reproducible environments and commands say through Miniconda/bioconda?
from leafcutter.
Same thing when I try installing from within R:
> install.packages('rstan', 'foreach', 'ggplot2', 'R.utils', 'gridExtra', 'reshape2', 'Hmisc', 'dplyr', 'doMC', 'optparse')
Warning in install.packages("rstan", "foreach", "ggplot2", "R.utils", "gridExtra", :
'lib = "foreach"' is not writable
Would you like to use a personal library instead? (y/n) y
Would you like to create a personal library
~/R/x86_64-pc-linux-gnu-library/3.3
to install packages into? (y/n) y
Error in available[p1, dependencies, drop = FALSE] :
incorrect number of dimensions
In addition: Warning message:
package ‘rstan’ is not available (for R version 3.3.1)
from leafcutter.
Ug don't know how I missed this thread, sorry! Did you ever manage to get the installation to work? If you're still interested please can you try
library(devtools)
install_github("davidaknowles/leafcutter/leafcutter")
and let me know if that works?
It's strange that your R couldn't find rstan
, it only requires R>=3.0.2. Out of curiosity were you trying to do this on a remote cluster? Sometimes I've noticed explicitly setting the repo
helps, e.g.
install.packages('rstan', repos='http://cran.us.r-project.org')
I can look at building a conda package but it's a bit discouraging if it can't even handle the dependencies!
from leafcutter.
We do now have a(n experimental) conda package:
conda install -c davidaknowles r-leafcutter
from leafcutter.
Closing this since the devtools
and conda
options should have addressed it.
from leafcutter.
@davidaknowles
I am sorry that I met the problem when I try to install the leafcutter package by 'devtools'. The details are showing below.
And I also tried the second method, which is to install from source. After I installed all the required packages in r, and run the instructed command. I got the error as below.
I am using system macOS 10.13.4.
Could you please help me to solve this problem?
Thank you very much for your time and patience.
from leafcutter.
Also having issues using R 3.5.1 and macOS 10.13.4 with both ways from the READ_ME with a number of errors. I've installed all packages manually as well. Error messages are the same for both the R install and terminal install.
In file included from Modules.cpp:3:
In file included from ./include/models.hpp:21:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:162:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_multiply.hpp:5:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:20:10: error:
unknown type name 'constexpr'
static constexpr int p_max = 8;
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:20:20: error:
expected member name or ';' after declaration specifiers
static constexpr int p_max = 8;
~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:21:10: error:
unknown type name 'constexpr'
static constexpr int m_max = 55;
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:21:20: error:
expected member name or ';' after declaration specifiers
static constexpr int m_max = 55;
~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:22:10: error:
unknown type name 'constexpr'
static constexpr double tol = 1.1e-16;
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:22:20: error:
expected member name or ';' after declaration specifiers
static constexpr double tol = 1.1e-16;
~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:25:29: error:
function definition does not declare parameters
const std::vector<double> theta_m_single_precision{
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:28:29: error:
function definition does not declare parameters
const std::vector<double> theta_m_double_precision{
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
from leafcutter.
This should be fixed now. stan
has changed how the package structure works and requires C++11.
from leafcutter.
Related Issues (20)
- confusion of normalization method for sQTL input date prepare HOT 1
- Alternative splicing signal on tandem duplicated genes HOT 1
- Creating co-splicing networks with leafcutter output?
- this is broken
- differential splicing with continuous independent variable
- Positive splicing events are not be detected HOT 2
- Start and end sites of junctions
- more than one genes in one cluster
- leafviz error HOT 9
- Intron Clustering HOT 5
- Junc files include one strand HOT 2
- question regarding the AS types (paper supplementary figure1)
- Error report for $bam2junc.sh
- an error about leafcutter_cluster.py HOT 4
- question regarding p-value for each intron usage
- Unable to install leafcutter R 4.2.1 HOT 8
- ENSG id and gene name not matching HOT 1
- Devtools installing LeafCutter Error HOT 5
- Delta psi is inconsistent in Leafviz HOT 1
- leafviz visualization does not show gene names HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from leafcutter.