@@ -1,6 +1,6 @@

 Package: seqbias

-Version: 1.33.0

-Date: 2019-03-15

+Version: 1.33.1

+Date: 2019-10-12

 Title: Estimation of per-position bias in high-throughput sequencing

         data

 Description: This package implements a model of per-position sequencing

@@ -12,6 +12,7 @@ Maintainer: Daniel Jones <dcjones@cs.washington.edu>

 Depends: R (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>=

         2.15.0), methods

 LinkingTo: Rhtslib (>= 1.15.3)

+SystemRequirements: GNU make

 Suggests: Rsamtools, ggplot2

 LazyLoad: yes

 License: LGPL-3

@@ -1,9 +1,13 @@

+## This file uses GNU make syntax $(shell ...) so we need to

+## have "SystemRequirements: GNU make" in the DESCRIPTION file.

+## See Rhtslib's vignette for details.

+

 include Makevars.common

-RHTSLIB_LIBS=`echo 'Rhtslib::pkgconfig("PKG_LIBS")'|\

-    "${R_HOME}/bin/R" --vanilla --slave`

-RHTSLIB_CPPFLAGS=`echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'|\

-    "${R_HOME}/bin/R" --vanilla --slave`

+RHTSLIB_LIBS=$(shell echo 'Rhtslib::pkgconfig("PKG_LIBS")'|\

+    "${R_HOME}/bin/R" --vanilla --slave)

+RHTSLIB_CPPFLAGS=$(shell echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'|\

+    "${R_HOME}/bin/R" --vanilla --slave)

 PKG_LIBS=$(RHTSLIB_LIBS)

 PKG_CPPFLAGS=$(RHTSLIB_CPPFLAGS)

deleted file mode 100644

@@ -1,17 +0,0 @@

-include Makevars.common

-

-RHTSLIB_LIBS=$(shell echo 'Rhtslib::pkgconfig("PKG_LIBS")'|\

-    "${R_HOME}/bin/R" --vanilla --slave)

-RHTSLIB_CPPFLAGS=$(shell echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'|\

-    "${R_HOME}/bin/R" --vanilla --slave)

-

-PKG_LIBS=$(RHTSLIB_LIBS)

-PKG_CPPFLAGS=$(RHTSLIB_CPPFLAGS)

-

-OBJECTS = $(SEQBIAS_OBJ) $(YAML_CPP_OBJ:%=yaml-cpp/%)

-

-all : $(SHLIB)

-

-clean :

-	rm -rf $(OBJECTS)

-