Java error in opening the DNA file

[r4work]

Hi I am using Mac OS. rDNA worked fine until yesterday. Now, it is throwing this error message as soon as I try executing command dna_gui(dna_sample())

Error: A JNI error has occurred, please check your installation and try again Exception in thread "main" java.lang.UnsupportedClassVersionError: dna/Dna has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0

I also updated Java on my Mac. Please suggest solution.

[leifeld]

It sounds like you were using the 2.0 version of rDNA with the 2.0 version of the jar file (which is fine), but then somehow the 3.0 version of the jar file sneaked into either the installation directory or working directory of rDNA. This can happen if you use dna_sample or dna_init with the force argument or if you use dna_download. You need to delete the 3.0 version of the jar file. See here for instructions. I will create a better 3.0 version of rDNA in the next month.

[r4work]

It sounds like you were using the 2.0 version of rDNA with the 2.0 version of the jar file (which is fine), but then somehow the 3.0 version of the jar file sneaked into either the installation directory or working directory of rDNA. This can happen if you use dna_sample or dna_init with the force argument or if you use dna_download. You need to delete the 3.0 version of the jar file. See here for instructions. I will create a better 3.0 version of rDNA in the next month.

Thank you Prof Leifeld. I removed the DNA-3.0 file from the installation directory and supplied the DNA 2.0 file to my working directory. Then the dna_gui(infile="filename.dna")) worked and I could navigate my coded file. Unfortunately, it now throws the following error when I type dna_connection(infile="filename.dna")

java.io.FileNotFoundException: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rDNA/extdata/dna-3.0.8.jar (No such file or directory) java.io.FileNotFoundException: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rDNA/extdata/dna-3.0.8.jar (No such file or directory) java.io.FileNotFoundException: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rDNA/extdata/dna-3.0.8.jar (No such file or directory) at java.util.zip.ZipFile.open(Native Method) at java.util.zip.ZipFile.(ZipFile.java:226) at java.util.zip.ZipFile.(ZipFile.java:155) at java.util.jar.JarFile.(JarFile.java:170) at java.util.jar.JarFile.(JarFile.java:107) at sun.net.www.protocol.jar.URLJarFile.(URLJarFile.java:93) at sun.net.www.protocol.jar.URLJarFile.getJarFile(URLJarFile.java:69) at sun.net.www.protocol.jar.JarFileFactory.get(JarFileFactory.java:168) at sun.net.www.protocol.jar.JarFileFactory.getOrCreate(JarFileFactory.java:91) at sun.net.www.protocol.jar.JarURLConnection.connect(JarURLConnection.java:129) at sun.net.www.protocol.jar.JarURLConnection.getInputStream(JarURLConnection.java:172) at org.sqlite.SQLiteJDBCLoader.getResourceAsStream(SQLiteJDBCLoader.java:280) at org.sqlite.SQLiteJDBCLoader.extractAndLoadLibraryFile(SQLiteJDBCLoader.java:208) at org.sqlite.SQLiteJDBCLoader.loadSQLiteNativeLibrary(SQLiteJDBCLoader.java:366) at org.sqlite.SQLiteJDBCLoader.initialize(SQLiteJDBCLoader.java:68) at org.sqlite.core.NativeDB.load(NativeDB.java:63) at org.sqlite.SQLiteConnection.open(SQLiteConnection.java:240) at org.sqlite.SQLiteConnection.(SQLiteConnection.java:61) at org.sqlite.jdbc3.JDBC3Connection.(JDBC3Connection.java:28) at org.sqlite.jdbc4.JDBC4Connection.(JDBC4Connection.java:21) at org.sqlite.JDBC.createConnection(JDBC.java:115) at org.sqlite.JDBC.connect(JDBC.java:90) at java.sql.DriverManager.getConnection(DriverManager.java:664) at java.sql.DriverManager.getConnection(DriverManager.java:270) at dna.SqlConnection.(SqlConnection.java:55) at dna.export.ExporterR.(ExporterR.java:84) java.sql.SQLException: Error opening connection at org.sqlite.SQLiteConnection.open(SQLiteConnection.java:244) at org.sqlite.SQLiteConnection.(SQLiteConnection.java:61) at org.sqlite.jdbc3.JDBC3Connection.(JDBC3Connection.java:28) at org.sqlite.jdbc4.JDBC4Connection.(JDBC4Connection.java:21) at org.sqlite.JDBC.createConnection(JDBC.java:115) at org.sqlite.JDBC.connect(JDBC.java:90) at java.sql.DriverManager.getConnection(DriverManager.java:664) at java.sql.DriverManager.getConnection(DriverManager.java:270) at dna.SqlConnection.(SqlConnection.java:55) at dna.export.ExporterR.(ExporterR.java:84) Caused by: java.lang.NullPointerException at org.sqlite.SQLiteJDBCLoader.extractAndLoadLibraryFile(SQLiteJDBCLoader.java:216) at org.sqlite.SQLiteJDBCLoader.loadSQLiteNativeLibrary(SQLiteJDBCLoader.java:366) at org.sqlite.SQLiteJDBCLoader.initialize(SQLiteJDBCLoader.java:68) at org.sqlite.core.NativeDB.load(NativeDB.java:63) at org.sqlite.SQLiteConnection.open(SQLiteConnection.java:240) ... 9 more Error in dna_connection(infile = "filename.dna") : java.lang.NullPointerException

Looking forward to your expert suggestion.

[leifeld]

Close DNA and R. Then make sure the DNA 2.0 jar file is in the inst directory of the rDNA installation path and no other jar file is there. Then make sure there is no jar file in the working directory. Then start R and verify using packageVersion("rDNA") that you have the rDNA 2 (not 3) installed. Try loading the package, initializing the jar file, and connecting to a version 2 database. Does this work? If not, which step fails?

[r4work]

It worked!

Thank you very much Prof. Leifeld.

[leifeld]

Great! All the best for your analysis!