Compile error

[Anonymous]

Hi!
I am trying to use your software for analysis and assembly purposes, but I encountered an error while attempting to compile the code.
I obtained the code using the command: git clone https://github.com/NGSEP/NGSEPcore.git
Later, when I tried to compile it using the command "make all", the terminal displayed the following error messages:

rm -f NGSEPcore_4.3.2.jar
rm -rf bin
mkdir bin
javac -cp lib/jsci-core.jar:lib/htsjdk-2.22.jar -d bin src/ngsep/.java src/ngsep//.java src/ngsep///.java
src/ngsep/clustering/DistanceClusteringService.java:21: error: cannot find symbol
private static final Set<integer> ALG_OPTIONS = Set.of(
^
symbol: method of(int,int)
location: interface Set
src/ngsep/clustering/dendrogram/Dendrogram.java:85: error: cannot find symbol
return new Dendrogram(name, List.of(
^
symbol: method of(DendrogramEdge,DendrogramEdge)
location: interface List
src/ngsep/genome/GenomeAssemblyMask.java:160: error: cannot find symbol
String nString = "N".repeat(endZeroBased-nextPos);
^
symbol: method repeat(int)
location: class String
3 errors
makefile:8: recipe for target 'compile' failed
make: *** [compile] Error 1</integer>

Could you please assist me in resolving this issue?
Thank you!

[Diego Almansa-Villa]

Hi!
I am trying to use your software for analysis and assembly purposes, but I encountered an error while attempting to compile the code.
I obtained the code using the command: git clone https://github.com/NGSEP/NGSEPcore.git
Later, when I tried to compile it using the command "make all", the terminal displayed the following error messages:

rm -f NGSEPcore_4.3.2.jar
rm -rf bin
mkdir bin
javac -cp lib/jsci-core.jar:lib/htsjdk-2.22.jar -d bin src/ngsep/.java src/ngsep//.java src/ngsep///.java
src/ngsep/clustering/DistanceClusteringService.java:21: error: cannot find symbol
private static final Set<integer> ALG_OPTIONS = Set.of(
^
symbol: method of(int,int)
location: interface Set
src/ngsep/clustering/dendrogram/Dendrogram.java:85: error: cannot find symbol
return new Dendrogram(name, List.of(
^
symbol: method of(DendrogramEdge,DendrogramEdge)
location: interface List
src/ngsep/genome/GenomeAssemblyMask.java:160: error: cannot find symbol
String nString = "N".repeat(endZeroBased-nextPos);
^
symbol: method repeat(int)
location: class String
3 errors
makefile:8: recipe for target 'compile' failed
make: *** [compile] Error 1</integer>

Could you please assist me in resolving this issue?
Thank you!

[Jorge Duitama]

Hi Diego

Thanks for your interest in NGSEP. As a user, you do not need to recompile the software. I recommend you to download and run the official version 4.3.1. For this, you just need the file NGSEPcore_4.3.1.jar, available either as part of the source code or directly in the files folder. You can download the live development cloning the git repository and build the version 4.3.2, but I must warn you that this version can have errors because we have not performed a full test run on this version.

That being said, I could clone the repository and compile the software using the JDK v 11. Please let me know the version of the JDK that you have installed. You can know that by running javac -version.

[Diego Almansa-Villa]

Thanks, it works for me!