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olgabot avatar olgabot commented on July 18, 2024

Any suggestions?

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olgabot avatar olgabot commented on July 18, 2024

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?

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olgabot avatar olgabot commented on July 18, 2024

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) 

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davidaknowles avatar davidaknowles commented on July 18, 2024

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!

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davidaknowles avatar davidaknowles commented on July 18, 2024

We do now have a(n experimental) conda package:
conda install -c davidaknowles r-leafcutter

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davidaknowles avatar davidaknowles commented on July 18, 2024

Closing this since the devtools and conda options should have addressed it.

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mikexjiang avatar mikexjiang commented on July 18, 2024

@davidaknowles
I am sorry that I met the problem when I try to install the leafcutter package by 'devtools'. The details are showing below.

screen shot 2018-05-11 at 12 08 48

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.
screen shot 2018-05-11 at 12 14 16

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.

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raungar avatar raungar commented on July 18, 2024

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=]

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davidaknowles avatar davidaknowles commented on July 18, 2024

This should be fixed now. stan has changed how the package structure works and requires C++11.

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