Building Adam on OS X 10.10.5 with Java 1.8 #835

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dbl001 opened this Issue Sep 27, 2015 · 5 comments

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@dbl001

dbl001 commented Sep 27, 2015

Hi,

I recently downgraded Adam to version 1.6 because of a problem with the method: adamLoad().
:20: error: value adamLoad is not a member of org.apache.spark.SparkContext

git clone -b adam-parent-0.16.0 https://github.com/bigdatagenomics/adam.git

Now, I'm having problems building adam with Java 1.8:

$ java -version
java version "1.8.0_05"
Java(TM) SE Runtime Environment (build 1.8.0_05-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.5-b02, mixed mode)
David-Laxers-MacBook-Pro:adam davidlaxer$ mvn -version
Apache Maven 3.2.1 (ea8b2b07643dbb1b84b6d16e1f08391b666bc1e9; 2014-02-14T09:37:52-08:00)
Maven home: /Users/davidlaxer/Downloads/apache-maven-3.2.1
Java version: 1.8.0_05, vendor: Oracle Corporation
Java home: /Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "mac os x", version: "10.10.5", arch: "x86_64", family: "mac"
  1. Can Adam 1.6 be built with Java 1.8?
  2. What's the replacement for the adamLoad() method in the current version of adam?
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fnothaft Sep 27, 2015

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Hi @dbl001 !

What sort of data are you trying to load? (e.g., read, variant, etc) We changed adamLoad to specific functions per each datatype (this made type checks cleaner), e.g., loadAlignments for reads, loadGenotypes for genotypes, loadVariants for variants, loadSequence for contigs, etc.

I'm not sure about 0.16.0, but I do know that the current ToT can be used with Java 1.8. IIRC, we added Java 8 support in ADAM 0.17.0.

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fnothaft commented Sep 27, 2015

Hi @dbl001 !

What sort of data are you trying to load? (e.g., read, variant, etc) We changed adamLoad to specific functions per each datatype (this made type checks cleaner), e.g., loadAlignments for reads, loadGenotypes for genotypes, loadVariants for variants, loadSequence for contigs, etc.

I'm not sure about 0.16.0, but I do know that the current ToT can be used with Java 1.8. IIRC, we added Java 8 support in ADAM 0.17.0.

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dbl001 Sep 27, 2015

Hi,

Thanks for the quick response!

I’m working through Chapter 10 of ‘Advanced Analytics with Spark’.
The data was /users/davidlaxer/genomics/HG00103.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam,
which I converted with ‘adam’ to parquet format in HDFS.

Don’t know if you can see the screen snapshot below:

On Sep 26, 2015, at 7:20 PM, Frank Austin Nothaft notifications@github.com wrote:

Hi @dbl001 https://github.com/dbl001 !

What sort of data are you trying to load? (e.g., read, variant, etc) We changed adamLoad to specific functions per each datatype (this made type checks cleaner), e.g., loadAlignments for reads https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L581, loadGenotypes for genotypes https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L555, loadVariants for variants https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L568, loadSequence for contigs https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L540, etc.

I'm not sure about 0.16.0, but I do know that the current ToT can be used with Java 1.8. IIRC, we added Java 8 support in ADAM 0.17.0.


Reply to this email directly or view it on GitHub #835 (comment).

dbl001 commented Sep 27, 2015

Hi,

Thanks for the quick response!

I’m working through Chapter 10 of ‘Advanced Analytics with Spark’.
The data was /users/davidlaxer/genomics/HG00103.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam,
which I converted with ‘adam’ to parquet format in HDFS.

Don’t know if you can see the screen snapshot below:

On Sep 26, 2015, at 7:20 PM, Frank Austin Nothaft notifications@github.com wrote:

Hi @dbl001 https://github.com/dbl001 !

What sort of data are you trying to load? (e.g., read, variant, etc) We changed adamLoad to specific functions per each datatype (this made type checks cleaner), e.g., loadAlignments for reads https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L581, loadGenotypes for genotypes https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L555, loadVariants for variants https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L568, loadSequence for contigs https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L540, etc.

I'm not sure about 0.16.0, but I do know that the current ToT can be used with Java 1.8. IIRC, we added Java 8 support in ADAM 0.17.0.


Reply to this email directly or view it on GitHub #835 (comment).

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dbl001 Sep 27, 2015

Spark 1.5
Hadoop 3.0 Snapshot
Maven 3.2.1
Java 1.8

On Sep 26, 2015, at 7:26 PM, David Laxer davidl@softintel.com wrote:

Hi,

Thanks for the quick response!

I’m working through Chapter 10 of ‘Advanced Analytics with Spark’.
The data was /users/davidlaxer/genomics/HG00103.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam,
which I converted with ‘adam’ to parquet format in HDFS.

Don’t know if you can see the screen snapshot below:

<Screen Shot 2015-09-26 at 7.25.27 PM.png>

On Sep 26, 2015, at 7:20 PM, Frank Austin Nothaft <notifications@github.com mailto:notifications@github.com> wrote:

Hi @dbl001 https://github.com/dbl001 !

What sort of data are you trying to load? (e.g., read, variant, etc) We changed adamLoad to specific functions per each datatype (this made type checks cleaner), e.g., loadAlignments for reads https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L581, loadGenotypes for genotypes https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L555, loadVariants for variants https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L568, loadSequence for contigs https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L540, etc.

I'm not sure about 0.16.0, but I do know that the current ToT can be used with Java 1.8. IIRC, we added Java 8 support in ADAM 0.17.0.


Reply to this email directly or view it on GitHub #835 (comment).

dbl001 commented Sep 27, 2015

Spark 1.5
Hadoop 3.0 Snapshot
Maven 3.2.1
Java 1.8

On Sep 26, 2015, at 7:26 PM, David Laxer davidl@softintel.com wrote:

Hi,

Thanks for the quick response!

I’m working through Chapter 10 of ‘Advanced Analytics with Spark’.
The data was /users/davidlaxer/genomics/HG00103.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam,
which I converted with ‘adam’ to parquet format in HDFS.

Don’t know if you can see the screen snapshot below:

<Screen Shot 2015-09-26 at 7.25.27 PM.png>

On Sep 26, 2015, at 7:20 PM, Frank Austin Nothaft <notifications@github.com mailto:notifications@github.com> wrote:

Hi @dbl001 https://github.com/dbl001 !

What sort of data are you trying to load? (e.g., read, variant, etc) We changed adamLoad to specific functions per each datatype (this made type checks cleaner), e.g., loadAlignments for reads https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L581, loadGenotypes for genotypes https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L555, loadVariants for variants https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L568, loadSequence for contigs https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L540, etc.

I'm not sure about 0.16.0, but I do know that the current ToT can be used with Java 1.8. IIRC, we added Java 8 support in ADAM 0.17.0.


Reply to this email directly or view it on GitHub #835 (comment).

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fnothaft Sep 27, 2015

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Hmmm, the snapshot didn't come across. Can you try again? If not, you can feel free to email it to me and I will take a look (probably tomorrow).

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fnothaft commented Sep 27, 2015

Hmmm, the snapshot didn't come across. Can you try again? If not, you can feel free to email it to me and I will take a look (probably tomorrow).

@dbl001 dbl001 referenced this issue in sryza/aas Sep 28, 2015

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Chapter 10: adamLoad() #45

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fnothaft Jul 6, 2016

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Closing as resolved/no additional follow up.

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fnothaft commented Jul 6, 2016

Closing as resolved/no additional follow up.

@fnothaft fnothaft closed this Jul 6, 2016

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