src/doc/issue_report_install.md

In leidenbase: R and C/C++ Wrappers to Run the Leiden find_partition() Function

Reporting Issues with Installing leidenbase

Please report issues with installing leidenbase using the leidenbase issues page on github.com.and please include the following information, which may help us to understand the problem

• computer system
• R installation
• R sessionInfo()
• describe the error

Computer system

I need to know the type, name, and version of your computer system. Is it MacOS, Linux, Windows, or some other system? Examples are

  Windows 10 Pro
  MacOS version 10.14
  Ubuntu Linux 18.04.3

In order to install leidenbase, you must have C, C++, and FORTRAN compilers installed on your system. Please check for them and report the names, locations, and versions of them, if possible.

Examples are

  language       some compiler commands
  --------       ----------------------
  C              cc, gcc, clang
  C++            c++, g++, clang++
  FORTRAN        f77, f95, gfortran, flang

If you installed any of the compilers manually or using a package manager, please include that information.

R installation

Please report your R version and how you installed it on your system. Did you build R manually from source code, install a package from CRAN, or build or install from another repository or package manager, for example, Homebrew?

If possible, please include information from the file called 'Makeconf', which is part of the R installation. This file is found usually either in the directory or a subdirectory of R_HOME/etc, where R_HOME is a directory path that you can find using the R command R.home().

The helpful lines in this file start with the strings

CC =
CFLAGS =
CPICFLAGS =
CPPFLAGS =
CXX =
CXXCPP =
CXXFLAGS =
CXXPICFLAGS =
CXX98 =
CXX98FLAGS =
CXX98PICFLAGS =
CXX98STD =
CXX11 =
CXX11FLAGS =
CXX11PICFLAGS =
CXX11STD =
CXX14 =
CXX14FLAGS =
CXX14PICFLAGS =
CXX14STD =
CXX17 =
CXX17FLAGS =
CXX17PICFLAGS =
CXX17STD =
CXX_VISIBILITY =
DYLIB_EXT =
DYLIB_LD =
DYLIB_LDFLAGS =
DYLIB_LINK =
FC =
FCFLAGS =
FCLIBS_XTRA =
FFLAGS =
FLIBS =

R sessionInfo

Please report the information from the R command 'sessionInfo()'.

Describe the error

Please report the error and post relevant output.

If possible, please include the full output of the install command, which you can get by

• download the leidenbase release as a .tar.gz file, which you can get from https://github.com/cole-trapnell-lab/leidenbase/releases
• in a terminal running the bash shell, go to the directory where you have the leidenbase release file
• run the following command (the release file at the time of writing is leidenbase-0.1.0.tar.gz, you may need to change this name if there is a more recent release)

R CMD INSTALL leidenbase-0.1.0.tar.gz > install.out 2>&1

• attach the resulting install.out file to your issue report

Thank you

I appreciate your feedback and patience.

leidenbase documentation built on April 3, 2025, 11:44 p.m.