<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.1.2">
        <repository name="package_r_3_1_2" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="limma" version="3.9.9">
        <install version="1.0">
            <actions>
                <action type="setup_r_environment">
                    <repository name="package_r_3_1_2" owner="iuc">
                        <package name="R" version="3.1.2" />
                    </repository>
                    <!-- bioarchive.github.io -->
                    <package>http://bioarchive.s3-website-us-east-1.amazonaws.com/limma_3.9.9.tar.gz</package>
                </action>
            </actions>
        </install>
        <readme>
Bioconductor package: Data analysis, linear models and differential expression for microarray data.
        </readme>
    </package>
</tool_dependency>

<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.1.2">
        <repository name="package_r_3_1_2" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="limma" version="3.9.9">
        <install version="1.0">
            <actions>
                <action type="setup_r_environment">
                    <repository name="package_r_3_1_2" owner="iuc">
                        <package name="R" version="3.1.2" />
                    </repository>
                    <!-- bioarchive.github.io -->
                    <package>http://bioarchive.s3-website-us-east-1.amazonaws.com/limma_3.25.3.tar.gz</package>
                </action>
            </actions>
        </install>
        <readme>
Bioconductor package: Data analysis, linear models and differential expression for microarray data.
        </readme>
    </package>
</tool_dependency>

Upgrade to more recent limma packaeg which plays nicely with edgeR3.9.9
Upgrade to more recent limma packaeg which plays nicely with edgeR3.9.9
