I tried compiling jvarkit and got the following error (only last ~25 lines reproduced below), the make then quit.

htsjdk-jar:
    [mkdir] Created dir: /Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist
      [jar] Building jar: /Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist/htsjdk-1.139.jar
     [copy] Copying 6 files to /Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist

all:

BUILD SUCCESSFUL
Total time: 15 seconds
touch -c /Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist/commons-jexl-2.1.1.jar
mkdir -p /Users/bertgold/Documents/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/
echo "package com.github.lindenb.jvarkit.util.htsjdk;" > /Users/bertgold/Documents/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo '@javax.annotation.Generated("jvarkit")' >> /Users/bertgold/Documents/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public class HtsjdkVersion{ private HtsjdkVersion(){}' >> /Users/bertgold/Documents/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public static String getVersion() {return "1.139";}' >> /Users/bertgold/Documents/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public static String getHome() {return "/Users/bertgold/Documents/jvarkit/htsjdk-1.139";}' >> /Users/bertgold/Documents/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public static String getJavadocUrl(Class clazz) {return "https://samtools.github.io/htsjdk/javadoc/htsjdk/"+clazz.getName().replaceAll("\\.","/")+".html";}' >> /Users/bertgold/Documents/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo '}'  >> /Users/bertgold/Documents/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
mkdir -p lib/commons-cli/commons-cli/1.3.1/ && curl -Lk  -o "lib/commons-cli/commons-cli/1.3.1/commons-cli-1.3.1.jar" "http://central.maven.org/maven2/commons-cli/commons-cli/1.3.1/commons-cli-1.3.1.jar"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
curl: (52) Empty reply from server
make: *** [lib/commons-cli/commons-cli/1.3.1/commons-cli-1.3.1.jar] Error 52

I'm still having problems...

Again, just the last few lines, where it's failing:

javac -version
javac 1.6.0_65
#compile
javac -d /Users/bertgold/Documents/jvarkit/_tmp-1.139 -g -classpath "/Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist/commons-jexl-2.1.1.jar:/Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist/commons-logging-1.1.1.jar:/Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist/htsjdk-1.139.jar:/Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist/snappy-java-1.0.3-rc3.jar:/Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist/commons-compress-1.4.1.jar:/Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist/apache-ant-1.8.2-bzip2.jar:/Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist/xz-1.5.jar:lib/commons-cli/commons-cli/1.3.1/commons-cli-1.3.1.jar" -sourcepath /Users/bertgold/Documents/jvarkit/src/main/java:/Users/bertgold/Documents/jvarkit/src/main/generated-sources/java /Users/bertgold/Documents/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java /Users/bertgold/Documents/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/backlocate/BackLocate.java
/Users/bertgold/Documents/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/backlocate/BackLocate.java:67: illegal start of type
        private Map<String,Set<String>> geneSymbol2kg=new HashMap<>();
                                                                  ^
/Users/bertgold/Documents/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/backlocate/BackLocate.java:68: illegal start of type
        private Map<String,KnownGene> knwonGenes=new HashMap<>();
                                                             ^
/Users/bertgold/Documents/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/backlocate/BackLocate.java:262: illegal start of type
        final Set<String> possibleAltCodons = new HashSet<>();
                                                          ^
3 errors
make: *** [backlocate] Error 1