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smirarab / ASTRAL

Accurate Species TRee ALgorithm
Apache License 2.0
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compilation error: Source option 6 is no longer supported. Use 7 or later. #86

Open jaum20 opened 1 year ago

jaum20 commented 1 year ago

Describe the bug A clear and concise description of what the bug is.

the program fails to compile

To Reproduce Give exact command you ran. When you run ASTRAL, make sure you keep the standard error (e.g., by adding 2>astral.log to the end of your command).

git clone https://github.com/smirarab/ASTRAL cd ASTRAL ./make.sh

Log file Send us the log file (standard error of ASTRAL)

++ grep _versinon main/phylonet/coalescent/CommandLine.java
++ grep String
++ sed -e 's/.*= .//g' -e 's/.;//g'
+ version=5.7.8
+ echo Version 5.7.8
Version 5.7.8
+ cd main
+ rm -f 'phylonet/coalescent/*.class' phylonet/util/BitSet.class 'phylonet/tree/model/sti/STITreeCluster*.class' phylonet/tree/io/NewickWriter.class
+ javac -source 1.6 -target 1.6 -classpath ../lib/main.jar:../lib/colt.jar:../lib/JSAP-2.1.jar phylonet/util/BitSet.java phylonet/coalescent/AbstractClusterCollection.java phylonet/coalescent/AbstractComputeMinCostTask.java phylonet/coalescent/AbstractDataCollection.java phylonet/coalescent/AbstractInference.java phylonet/coalescent/AbstractPartition.java phylonet/coalescent/AbstractWeightCalculator.java phylonet/coalescent/BipartitionWeightCalculator.java phylonet/coalescent/CannotResolveException.java phylonet/coalescent/CommandLine.java phylonet/coalescent/DeepCoalescencesCounter.java phylonet/coalescent/DLClusterCollection.java phylonet/coalescent/DLComputeMinCostTask.java phylonet/coalescent/DLDataCollection.java phylonet/coalescent/DLInference.java phylonet/coalescent/DLWeightCalculator.java phylonet/coalescent/GlobalMaps.java phylonet/coalescent/IClusterCollection.java phylonet/coalescent/Options.java phylonet/coalescent/Polytomy.java phylonet/coalescent/Polytree.java phylonet/coalescent/Posterior.java phylonet/coalescent/QuartetCollection.java phylonet/coalescent/SimilarityMatrix.java phylonet/coalescent/SingleIndividualSample.java phylonet/coalescent/Solution.java phylonet/coalescent/SpeciesMapper.java phylonet/coalescent/STBipartition.java phylonet/coalescent/TaxonIdentifier.java phylonet/coalescent/TaxonNameMap.java phylonet/coalescent/Tripartition.java phylonet/coalescent/Utils.java phylonet/coalescent/WQClusterCollection.java phylonet/coalescent/WQComputeMinCostTask.java phylonet/coalescent/WQDataCollection.java phylonet/coalescent/WQInference.java phylonet/coalescent/WQWeightCalculator.java phylonet/tree/model/sti/STITreeCluster.java phylonet/tree/io/NewickWriter.java
warning: [options] bootstrap class path not set in conjunction with -source 6
error: Source option 6 is no longer supported. Use 7 or later.
error: Target option 6 is no longer supported. Use 7 or later.

** Version

Additional context Add any other context about the problem here.

mbutler808 commented 1 year ago

Hi @jaum20 If you are on a Mac, I found online that you can install astral with homebrew. After installing homebrew (https://brew.sh) , open a terminal and run

brew install brewsci/bio/astral

It needs to be a recent OS, however. It installed on my machine running Ventura, but not Mojave

smirarab commented 1 year ago

Sorry for the delayed response.

Changing 1.6 to 1.7 in the line below should fix it:

https://github.com/smirarab/ASTRAL/blob/master/make.sh#L14

I keep this open so that I can fix it in future releases.