Hi,
last May I was seeking for help with megan-ce[1]. I tried to implement
all useful hints I've got and also the source code evolved since then.
In my current packaging[2] I get the following errors:
Buildfile: /build/megan-ce-0.0+git20180524.24e70bf/antbuild/build.xml
init:
[mkdir] Created dir: /build/megan-ce-0.0+git20180524.24e70bf/antbuild/src
[mkdir] Created dir:
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/classes
[mkdir] Created dir:
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/classes/resources
copy_resources:
[mkdir] Created dir:
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/classes/resources/css
[mkdir] Created dir:
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/classes/resources/files
[copy] Copying 1 file to
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/classes
copy_sources:
[copy] Copying 1247 files to
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src
copy_fx:
[copy] Copying 1 file to
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/classes
compile:
[javac] Compiling 1242 source files to
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/classes
[javac] warning: [options] bootstrap class path not set in conjunction with
-source 7
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2Importer.java:21:
error: package ch.systemsx.cisd.hdf5 does not exist
[javac] import ch.systemsx.cisd.hdf5.HDF5Factory;
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2Importer.java:22:
error: package ch.systemsx.cisd.hdf5 does not exist
[javac] import ch.systemsx.cisd.hdf5.IHDF5Reader;
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2MetaData.java:22:
error: package ch.systemsx.cisd.hdf5 does not exist
[javac] import ch.systemsx.cisd.hdf5.IHDF5Reader;
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2MetaData.java:23:
error: package ch.systemsx.cisd.hdf5 does not exist
[javac] import ch.systemsx.cisd.hdf5.IHDF5Writer;
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2MetaData.java:40:
error: cannot find symbol
[javac] public static int read(IHDF5Reader reader, String[] sampleIds,
SampleAttributeTable table) throws IOException {
[javac] ^
[javac] symbol: class IHDF5Reader
[javac] location: class Biom2MetaData
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2MetaData.java:62:
error: cannot find symbol
[javac] public static void write(IHDF5Writer writer, String[]
sampleIds, SampleAttributeTable table) throws IOException {
[javac] ^
[javac] symbol: class IHDF5Writer
[javac] location: class Biom2MetaData
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2ParserTest.java:22:
error: package ch.systemsx.cisd.base.mdarray does not exist
[javac] import ch.systemsx.cisd.base.mdarray.MDArray;
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2ParserTest.java:23:
error: package ch.systemsx.cisd.hdf5 does not exist
[javac] import ch.systemsx.cisd.hdf5.HDF5Factory;
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2ParserTest.java:24:
error: package ch.systemsx.cisd.hdf5 does not exist
[javac] import ch.systemsx.cisd.hdf5.IHDF5Reader;
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2ParserTest.java:185:
error: cannot find symbol
[javac] private static String[] getPath(MDArray<String> array, int row,
int cols) {
[javac] ^
[javac] symbol: class MDArray
[javac] location: class Biom2ParserTest
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/ImportBiom2Taxonomy.java:22:
error: package ch.systemsx.cisd.base.mdarray does not exist
[javac] import ch.systemsx.cisd.base.mdarray.MDArray;
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/ImportBiom2Taxonomy.java:23:
error: package ch.systemsx.cisd.hdf5 does not exist
[javac] import ch.systemsx.cisd.hdf5.IHDF5Reader;
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/ImportBiom2Taxonomy.java:40:
error: cannot find symbol
[javac] public static Map<Integer, float[]>
getClass2Samples2Counts(IHDF5Reader reader, int numberOfSamples, boolean
ignorePathAbove) throws IOException {
[javac] ^
[javac] symbol: class IHDF5Reader
[javac] location: class ImportBiom2Taxonomy
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/ImportBiom2Taxonomy.java:101:
error: cannot find symbol
[javac] private static String[] getPath(MDArray<String> array, int row,
int cols) {
[javac] ^
[javac] symbol: class MDArray
[javac] location: class ImportBiom2Taxonomy
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/ImportBiom2Taxonomy.java:114:
error: cannot find symbol
[javac] public static boolean hasTaxonomyMetadata(IHDF5Reader reader) {
[javac] ^
[javac] symbol: class IHDF5Reader
[javac] location: class ImportBiom2Taxonomy
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/TopLevelAttributes.java:22:
error: package ch.systemsx.cisd.hdf5 does not exist
[javac] import ch.systemsx.cisd.hdf5.IHDF5Reader;
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/TopLevelAttributes.java:23:
error: package ch.systemsx.cisd.hdf5 does not exist
[javac] import ch.systemsx.cisd.hdf5.IHDF5Writer;
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/TopLevelAttributes.java:83:
error: cannot find symbol
[javac] public TopLevelAttributes(IHDF5Reader reader) throws
IOException {
[javac] ^
[javac] symbol: class IHDF5Reader
[javac] location: class TopLevelAttributes
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/TopLevelAttributes.java:93:
error: cannot find symbol
[javac] public void read(IHDF5Reader reader) throws IOException {
[javac] ^
[javac] symbol: class IHDF5Reader
[javac] location: class TopLevelAttributes
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/TopLevelAttributes.java:112:
error: cannot find symbol
[javac] public void write(IHDF5Writer writer) throws IOException {
[javac] ^
[javac] symbol: class IHDF5Writer
[javac] location: class TopLevelAttributes
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/groups/commands/ComputeContrastsCommand.java:21:
error: package contrasts does not exist
[javac] import contrasts.Contrasts;
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2Importer.java:58:
error: cannot find symbol
[javac] try (IHDF5Reader reader =
HDF5Factory.openForReading(fileName)) {
[javac] ^
[javac] symbol: class IHDF5Reader
[javac] location: class Biom2Importer
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2Importer.java:58:
error: cannot find symbol
[javac] try (IHDF5Reader reader =
HDF5Factory.openForReading(fileName)) {
[javac] ^
[javac] symbol: variable HDF5Factory
[javac] location: class Biom2Importer
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2ParserTest.java:58:
error: cannot find symbol
[javac] try (IHDF5Reader reader =
HDF5Factory.openForReading(inputFile)) {
[javac] ^
[javac] symbol: class IHDF5Reader
[javac] location: class Biom2ParserTest
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2ParserTest.java:58:
error: cannot find symbol
[javac] try (IHDF5Reader reader =
HDF5Factory.openForReading(inputFile)) {
[javac] ^
[javac] symbol: variable HDF5Factory
[javac] location: class Biom2ParserTest
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2ParserTest.java:65:
error: cannot find symbol
[javac] final Map<String, MDArray<String>>
classification2MDArray = new HashMap<>();
[javac] ^
[javac] symbol: class MDArray
[javac] location: class Biom2ParserTest
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2ParserTest.java:75:
error: cannot find symbol
[javac] final MDArray<String> array =
reader.readStringMDArray("/observation/metadata/" + taxonomyNameMetadata);
[javac] ^
[javac] symbol: class MDArray
[javac] location: class Biom2ParserTest
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/Biom2ParserTest.java:121:
error: cannot find symbol
[javac] final MDArray<String> pathArray =
classification2MDArray.get(classificationName);
[javac] ^
[javac] symbol: class MDArray
[javac] location: class Biom2ParserTest
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/ImportBiom2Taxonomy.java:45:
error: cannot find symbol
[javac] MDArray<String> pathArray = null;
[javac] ^
[javac] symbol: class MDArray
[javac] location: class ImportBiom2Taxonomy
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/biom/biom2/ImportBiom2Taxonomy.java:117:
error: cannot find symbol
[javac] final MDArray<String> pathArray =
reader.readStringMDArray("/observation/metadata/" + metaKey);
[javac] ^
[javac] symbol: class MDArray
[javac] location: class ImportBiom2Taxonomy
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/groups/commands/ComputeContrastsCommand.java:114:
error: cannot find symbol
[javac] final Contrasts contrasts = new Contrasts();
[javac] ^
[javac] symbol: class Contrasts
[javac] location: class ComputeContrastsCommand
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/megan/groups/commands/ComputeContrastsCommand.java:114:
error: cannot find symbol
[javac] final Contrasts contrasts = new Contrasts();
[javac] ^
[javac] symbol: class Contrasts
[javac] location: class ComputeContrastsCommand
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/rusch/megan5client/connector/Megan5ServerConnector.java:72:
error: cannot access MultiValueMap
[javac] headers.add("Authorization", "Basic " + base64Creds);
[javac] ^
[javac] class file for org.springframework.util.MultiValueMap not found
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/rusch/megan5client/connector/Megan5ServerConnector.java:73:
error: incompatible types: HttpEntity<HttpHeaders> cannot be converted to
HttpEntity<String>
[javac] request = new HttpEntity<>(headers);
[javac] ^
[javac]
/build/megan-ce-0.0+git20180524.24e70bf/antbuild/src/rusch/megan5client/connector/Megan5ServerConnector.java:85:
error: cannot access ParameterizedTypeReference
[javac] url2response.put(requestURL,
restTemplate.exchange(requestURL, HttpMethod.GET, request,
RMADataset[].class).getBody());
[javac] ^
[javac] class file for
org.springframework.core.ParameterizedTypeReference not found
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -Xlint:deprecation for details.
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 35 errors
[javac] 1 warning
I think we should ignore the HDF5 related issues since this might be
connected to an issue in the used HDF5 library[3] (for sure I'd be happy
to receive hints about this as well but this should be separate :-) ).
I'd be really happy if I could get rid of all other (=non HDF5 related)
errors above. Any hint?
Kind regards
Andreas.
[1] https://lists.debian.org/debian-java/2017/05/msg00019.html
[2] https://salsa.debian.org/med-team/megan-ce
[3] https://lists.debian.org/debian-science/2018/05/msg00111.html
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