Merge branch 'dev'

CHANGELOG.md

@@ -1,5 +1,8 @@
 ## Upcoming
 
+## [1.5.2] - 2024-26-February
+- Removed `-L/usr/lib/` in Makevars
+
 ## [1.5.1] - 2024-22-January
 - Remove C++11 flag
 - Fixed various roxygen2 typos and variable names for docs consistency
@@ -23,9 +26,8 @@
 
 
 ## [1.4.6] - 2022-30-March
-
 - Fixed bug with `snn` argument in `buildGraph()` due to the parameter `snn.k.self`
-- Fixed bug in `getDifferentialGenes()` based on warnings from sccore::plapply()
+- Fixed bug in `getDifferentialGenes()` based on warnings from `sccore::plapply()`
 
 ## [1.4.5] - 2022-20-January
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: conos
 Title: Clustering on Network of Samples
-Version: 1.5.1
+Version: 1.5.2
 Authors@R: c(person("Viktor","Petukhov", email="[email protected]", role="aut"), person("Nikolas","Barkas", email="[email protected]", role="aut"), person("Peter", "Kharchenko", email = "[email protected]", role = "aut"), person("Weiliang", "Qiu", email = "[email protected]", role = c("ctb")), person("Evan", "Biederstedt", email="[email protected]", role=c("aut", "cre")))
 Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
 License: GPL-3

README.md

@@ -238,5 +238,5 @@ The R package can be cited as:
 ```
 Viktor Petukhov, Nikolas Barkas, Peter Kharchenko, and Evan
 Biederstedt (2021). conos: Clustering on Network of Samples. R
-package version 1.5.1.
+package version 1.5.2.
 ```

src/Makevars

@@ -1,2 +1,2 @@
 PKG_CXXFLAGS=-I"./include" $(SHLIB_OPENMP_CXXFLAGS) 
-PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
+PKG_LIBS=-L"." -lpthread -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)

src/Makevars.win

@@ -1,2 +1,2 @@
 PKG_CXXFLAGS=-I"./include" $(SHLIB_OPENMP_CXXFLAGS) 
-PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lm $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) 
+PKG_LIBS=-L"." -lpthread -lm $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)