[ADAM-1783] Resolve check issues that block pushing to CRAN. #1849
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Test FAILed. Build result: FAILURE[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1849/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 7c4f9a3 # timeout=10Checking out Revision 7c4f9a3 (origin/pr/1849/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 7c4f9a3328d1e79afb3b23f453e4ec0a1c7b338bFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
heuermh
requested changes
Jan 2, 2018
adam-r/bdgenomics.adam/R/rdd.R
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| #' @export | ||
| setClass("GenomicRDD", | ||
| slots = list(jrdd = "jobj")) | ||
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| #' A class that wraps DataFrame of genomic data with helpful metadata. |
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wraps DataFrame → wraps a DataFrame
adam-r/bdgenomics.adam/R/rdd.R
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| FeatureRDD <- function(jrdd) { | ||
| new("FeatureRDD", jrdd = jrdd) | ||
| } | ||
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| #' A class that wraps an RDD of read fragments with helpful metadata. |
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I find "read fragments" to be a bit confusing, but I suppose we use that elsewhere. "Read pairs grouped by sequencing fragment" is probably too verbose?
adam-r/bdgenomics.adam/R/rdd.R
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| @@ -474,89 +575,64 @@ setMethod("recalibrateBaseQualities", | |||
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| #' Realigns indels using a concensus-based heuristic. | |||
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As far as I know, SparkR ran into trouble with the CRAN submission process because Spark dropped temporary files in places it shouldn't. We might need to look out for the same. I had some Spark JIRA issues on the topic bookmarked but apparently not on this computer. |
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Test FAILed. Build result: FAILURE[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1849/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 9628690 # timeout=10Checking out Revision 9628690 (origin/pr/1849/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 962869088b4d0d35fc231fca86e3b0aa120fb6c0First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Jenkins, retest this please. |
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Test PASSed. |
heuermh
approved these changes
Jan 3, 2018
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As per discussion with @heuermh, we don't think we can push to CRAN until SparkR is back in CRAN due to: With SparkR being temporarily removed from CRAN, it is not available from a mainstream repository. The above snippet is from the CRAN policy guide. In lieu of CRAN, we will distribute the R tarball. |
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Resolves bigdatagenomics#1847. Cribs heavily from PySpark's script flow for supporting a full, self-contained pip install-able Spark by finding the JARs and bin scripts and packaging them up as packages which are deployed to pip. We then needed to modify the bin scripts to find the pip installed JARs.
Resolves bigdatagenomics#1783. Cleans up a host of documentation issues that would cause warnings when submitting to CRAN.
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Test PASSed. |
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Test PASSed. |
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Are twine and pypandoc supposed to be installed as part of the virtualenv? Then I suppose I should update the version in |
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Regarding |
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@heuermh I'd commit
No, you'll need to |
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ok, will try again this afternoon, and if it deploys to testpypi correctly, then I'll merge this pr and perform the release. |
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Back to my workstation, installed Miniconda for Python 2.7, sourced |
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Next tried installing pip, virtualenv, twine and pypandoc against system python, pandoc is |
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Ran Now having trouble with twine, created |
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DO |
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w00t! |
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Based on #1848. Resolves #1783 and #1847. Cleans up a host of documentation issues that would cause warnings when submitting to CRAN. TODO for tomorrow:
- [ ] Make sure that JAR is packaged in properly- [ ] Test on linux- [ ] Possibly test on Windows via CRAN windows test server- [ ] Add CRAN markdown readme