@@ -1,3 +1,10 @@

+version: 3.3.39

+date: 2019-2-20

+author: Tom Sherman <tomsherman159@gmail.com>

+

+    - fix bug when reading mtx and not ignoring comments

+    - allow setDistributedParams to be called to reset params

+

 version: 3.3.38

 date: 2019-2-18

 author: Tom Sherman <tomsherman159@gmail.com>

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

 Package: CoGAPS

-Version: 3.3.38

-Date: 2019-02-18

+Version: 3.3.39

+Date: 2019-02-20

 Title: Coordinated Gene Activity in Pattern Sets

 Author: Thomas Sherman, Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey,

     Genevieve Stein-O'Brien, Michael Considine, Maggie Wodicka, John Stansfield,

@@ -1,4 +1,4 @@

-# CoGAPS Version: 3.3.38

+# CoGAPS Version: 3.3.39

 [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)

 [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/)

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

 #! /bin/sh

 # Guess values for system-dependent variables and create Makefiles.

-# Generated by GNU Autoconf 2.69 for CoGAPS 3.3.38.

+# Generated by GNU Autoconf 2.69 for CoGAPS 3.3.39.

 #

 #

 # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.

@@ -577,8 +577,8 @@ MAKEFLAGS=

 # Identity of this package.

 PACKAGE_NAME='CoGAPS'

 PACKAGE_TARNAME='cogaps'

-PACKAGE_VERSION='3.3.38'

-PACKAGE_STRING='CoGAPS 3.3.38'

+PACKAGE_VERSION='3.3.39'

+PACKAGE_STRING='CoGAPS 3.3.39'

 PACKAGE_BUGREPORT=''

 PACKAGE_URL=''

@@ -1206,7 +1206,7 @@ if test "$ac_init_help" = "long"; then

   # Omit some internal or obsolete options to make the list less imposing.

   # This message is too long to be a string in the A/UX 3.1 sh.

   cat <<_ACEOF

-\`configure' configures CoGAPS 3.3.38 to adapt to many kinds of systems.

+\`configure' configures CoGAPS 3.3.39 to adapt to many kinds of systems.

 Usage: $0 [OPTION]... [VAR=VALUE]...

@@ -1268,7 +1268,7 @@ fi

 if test -n "$ac_init_help"; then

   case $ac_init_help in

-     short | recursive ) echo "Configuration of CoGAPS 3.3.38:";;

+     short | recursive ) echo "Configuration of CoGAPS 3.3.39:";;

    esac

   cat <<\_ACEOF

@@ -1359,7 +1359,7 @@ fi

 test -n "$ac_init_help" && exit $ac_status

 if $ac_init_version; then

   cat <<\_ACEOF

-CoGAPS configure 3.3.38

+CoGAPS configure 3.3.39

 generated by GNU Autoconf 2.69

 Copyright (C) 2012 Free Software Foundation, Inc.

@@ -1722,7 +1722,7 @@ cat >config.log <<_ACEOF

 This file contains any messages produced by compilers while

 running configure, to aid debugging if configure makes a mistake.

-It was created by CoGAPS $as_me 3.3.38, which was

+It was created by CoGAPS $as_me 3.3.39, which was

 generated by GNU Autoconf 2.69.  Invocation command line was

   $ $0 $@

@@ -4788,7 +4788,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1

 # report actual input values of CONFIG_FILES etc. instead of their

 # values after options handling.

 ac_log="

-This file was extended by CoGAPS $as_me 3.3.38, which was

+This file was extended by CoGAPS $as_me 3.3.39, which was

 generated by GNU Autoconf 2.69.  Invocation command line was

   CONFIG_FILES    = $CONFIG_FILES

@@ -4841,7 +4841,7 @@ _ACEOF

 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1

 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"

 ac_cs_version="\\

-CoGAPS config.status 3.3.38

+CoGAPS config.status 3.3.39

 configured by $0, generated by GNU Autoconf 2.69,

   with options \\"\$ac_cs_config\\"

@@ -6,11 +6,11 @@

 \alias{setDistributedParams,CogapsParams-method}

 \title{set the value of parameters for distributed CoGAPS}

 \usage{

-setDistributedParams(object, nSets, cut = NULL, minNS = NULL,

+setDistributedParams(object, nSets = NULL, cut = NULL, minNS = NULL,

   maxNS = NULL)

-\S4method{setDistributedParams}{CogapsParams}(object, nSets, cut = NULL,

-  minNS = NULL, maxNS = NULL)

+\S4method{setDistributedParams}{CogapsParams}(object, nSets = NULL,

+  cut = NULL, minNS = NULL, maxNS = NULL)

 }

 \arguments{

 \item{object}{an object of type CogapsParams}