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Error: Dependency package(s) 'SparkR' not available #2086

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heuermh opened this issue Nov 13, 2018 · 3 comments
Closed

Error: Dependency package(s) 'SparkR' not available #2086

heuermh opened this issue Nov 13, 2018 · 3 comments
Milestone
0.26.0

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@heuermh
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heuermh commented Nov 13, 2018

R build complains about not being able to find SparkR package

$ mvn -Pr package
...
[INFO] --- exec-maven-plugin:1.5.0:exec (doc-r) @ adam-r-spark2_2.11 ---

R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.7.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(devtools);devtools::document()
Updating bdgenomics.adam documentation
Updating roxygen version in adam/adam-r/bdgenomics.adam/DESCRIPTION
Writing NAMESPACE
Loading bdgenomics.adam
Error: Dependency package(s) 'SparkR' not available.
In addition: Warning messages:
1: roxygen2 requires Encoding: UTF-8
2: In (function (dep_name, dep_ver = "*")  :
  Dependency package 'SparkR' not available.
Execution halted
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)

I thought I had the SparkR package installed already, tried again, same result

SparkR
$ cd $SPARK_HOME/R/lib/SparkR/

SparkR
$ R -e "devtools::install('.')"

R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.7.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> devtools::install('.')
   checking for file ‘/usr/local/Cellar/apache-spark/2.3.2/libexec/R/lib/SparkR/✔  checking for file ‘/usr/local/Cellar/apache-spark/2.3.2/libexec/R/lib/SparkR/DESCRIPTION’
─  preparing ‘SparkR’:
✔  checking DESCRIPTION meta-information ...
   Warning in file(con, "r") :
     cannot open file 'man': No such file or directory
    ERROR
   computing Rd index failed:cannot open the connection
Error in run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout),  :
  System command error
Calls: <Anonymous> ... with.default -> eval -> eval -> with_envvar -> force -> run
Execution halted

SparkR
$ mkdir man

SparkR
$ R -e "devtools::install('.')"

R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.7.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> devtools::install('.')
   checking for file ‘/usr/local/Cellar/apache-spark/2.3.2/libexec/R/lib/SparkR/✔  checking for file ‘/usr/local/Cellar/apache-spark/2.3.2/libexec/R/lib/SparkR/DESCRIPTION’
─  preparing ‘SparkR’:
✔  checking DESCRIPTION meta-information ...
─  checking whether ‘INDEX’ is up-to-date ... NO
─  use ‘--force’ to remove the existing ‘INDEX’
─  excluding invalid files
   Subdirectory 'R' contains invalid file names:
     ‘SparkR’ ‘SparkR.rdb’ ‘SparkR.rdx’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Removed empty directory ‘SparkR/R’
   Removed empty directory ‘SparkR/man’
   WARNING: Removing directory ‘SparkR/Meta’ which should only occur in an
     installed package
   WARNING: Removing directory ‘SparkR/help’ which should only occur in an
     installed package
   WARNING: Removing directory ‘SparkR/html’ which should only occur in an
     installed package
─  building ‘SparkR_2.3.2.tar.gz’

Running /usr/local/Cellar/r/3.5.1/lib/R/bin/R CMD INSTALL \
  /var/folders/m6/4yqn_4q129lbth_dq3qzj_8h0000gn/T//RtmpkLFoFF/SparkR_2.3.2.tar.gz \
  --install-tests
* installing to library ‘/usr/local/lib/R/3.5/site-library’
* installing *binary* package ‘SparkR’ ...
* DONE (SparkR)

$ mvn -Pr package
...
[INFO] --- exec-maven-plugin:1.5.0:exec (doc-r) @ adam-r-spark2_2.11 ---

R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.7.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(devtools);devtools::document()
Updating bdgenomics.adam documentation
Loading bdgenomics.adam
Error: Dependency package(s) 'SparkR' not available.
In addition: Warning messages:
1: roxygen2 requires Encoding: UTF-8
2: In (function (dep_name, dep_ver = "*")  :
  Dependency package 'SparkR' not available.
Execution halted
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
@heuermh
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heuermh commented Nov 13, 2018

Some progress

$ R -e "devtools::install_github('apache/spark@v2.3.2', subdir='R/pkg')"

R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.7.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> devtools::install_github('apache/spark@v2.3.2', subdir='R/pkg')
Downloading GitHub repo apache/spark@v2.3.2
   checking for file ‘/private/var/folders/m6/4yqn_4q129lbth_dq3qzj_8h0000gn/T/Rtmp7pkOl3/remotes9efb2d5b4abf/apache-spark-02b5107/R/pkg/DESCR✔  checking for file ‘/private/var/folders/m6/4yqn_4q129lbth_dq3qzj_8h0000gn/T/Rtmp7pkOl3/remotes9efb2d5b4abf/apache-spark-02b5107/R/pkg/DESCRIPTION’
─  preparing ‘SparkR’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘SparkR_2.3.2.tar.gz’

Installing package into ‘/usr/local/lib/R/3.5/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘SparkR’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘as.data.frame’ in package ‘SparkR’
Creating a new generic function for ‘colnames’ in package ‘SparkR’
Creating a new generic function for ‘colnames<-’ in package ‘SparkR’
Creating a new generic function for ‘cov’ in package ‘SparkR’
Creating a new generic function for ‘drop’ in package ‘SparkR’
Creating a new generic function for ‘na.omit’ in package ‘SparkR’
Creating a new generic function for ‘filter’ in package ‘SparkR’
Creating a new generic function for ‘intersect’ in package ‘SparkR’
Creating a new generic function for ‘sample’ in package ‘SparkR’
Creating a new generic function for ‘transform’ in package ‘SparkR’
Creating a new generic function for ‘subset’ in package ‘SparkR’
Creating a new generic function for ‘summary’ in package ‘SparkR’
Creating a new generic function for ‘union’ in package ‘SparkR’
Creating a new generic function for ‘endsWith’ in package ‘SparkR’
Creating a new generic function for ‘startsWith’ in package ‘SparkR’
Creating a new generic function for ‘lag’ in package ‘SparkR’
Creating a new generic function for ‘rank’ in package ‘SparkR’
Creating a new generic function for ‘sd’ in package ‘SparkR’
Creating a new generic function for ‘var’ in package ‘SparkR’
Creating a new generic function for ‘window’ in package ‘SparkR’
Creating a new generic function for ‘predict’ in package ‘SparkR’
Creating a new generic function for ‘rbind’ in package ‘SparkR’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘%in%’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘Filter’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘factorial’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘atan2’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘SparkR’
** help
No man pages found in package  ‘SparkR’
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SparkR)

adam-r (HEAD detached at adam-parent-spark2_2.11-0.25.0)!
$ mvn -Pr package
[INFO] Scanning for projects...
[INFO]
[INFO] ---------------< org.bdgenomics.adam:adam-r-spark2_2.11 >---------------
[INFO] Building ADAM_2.11: R APIs 0.25.0-SNAPSHOT
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-r-spark2_2.11 ---
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-r-spark2_2.11 ---
[INFO]
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-r-spark2_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO]
[INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ adam-r-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory adam/adam-r/src/main/resources
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-r-spark2_2.11 ---
[INFO] No sources to compile
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (doc-r) @ adam-r-spark2_2.11 ---

R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.7.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(devtools);devtools::document()
Updating bdgenomics.adam documentation
Loading bdgenomics.adam
Creating a new generic function for ‘pipe’ in package ‘bdgenomics.adam’
Creating a new generic function for ‘transform’ in package ‘bdgenomics.adam’
Creating a new generic function for ‘save’ in package ‘bdgenomics.adam’
Creating a new generic function for ‘sort’ in package ‘bdgenomics.adam’

Attaching package: ‘SparkR’

The following objects are masked from ‘package:stats’:

    cov, filter, lag, na.omit, predict, sd, var, window

The following objects are masked from ‘package:base’:

    as.data.frame, colnames, colnames<-, drop, endsWith, intersect,
    rank, rbind, sample, startsWith, subset, summary, transform, union

Writing NAMESPACE
Writing ADAMContext.Rd
Writing GenomicDataset.Rd
Writing AlignmentRecordRDD.Rd
Writing CoverageRDD.Rd
Writing FragmentRDD.Rd
Writing toVariantContexts.Rd
Writing toVariants.Rd
Writing NucleotideContigFragmentRDD.Rd
Writing VariantContextRDD.Rd
Writing createADAMContext.Rd
Writing loadAlignments-ADAMContext-character-method.Rd
Writing loadContigFragments-ADAMContext-character-method.Rd
Writing loadFragments-ADAMContext-character-method.Rd
Writing loadFeatures-ADAMContext-character-method.Rd
Writing loadCoverage-ADAMContext-character-method.Rd
Writing loadGenotypes-ADAMContext-character-method.Rd
Writing loadVariants-ADAMContext-character-method.Rd
Writing FeatureRDD.Rd
Writing GenotypeRDD.Rd
Writing VariantRDD.Rd
Writing pipe-GenomicDataset-ANY-character-character-character-method.Rd
Writing cache-GenomicDataset-method.Rd
Writing persist-GenomicDataset-character-method.Rd
Writing unpersist-GenomicDataset-method.Rd
Writing sort-GenomicDataset-method.Rd
Writing sortLexicographically-GenomicDataset-method.Rd
Writing toDF-GenomicDataset-method.Rd
Writing transform-GenomicDataset-function-method.Rd
Writing transmute-GenomicDataset-function-character-method.Rd
Writing broadcastRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterBroadcastRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing broadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd
Writing shuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterShuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing leftOuterShuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing leftOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd
Writing fullOuterShuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd
Writing shuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd
Writing toFragments-AlignmentRecordRDD-method.Rd
Writing saveAsSam-AlignmentRecordRDD-character-method.Rd
Writing toCoverage-AlignmentRecordRDD-method.Rd
Writing save-AlignmentRecordRDD-character-method.Rd
Writing countKmers-AlignmentRecordRDD-numeric-method.Rd
Writing sortReadsByReferencePosition-AlignmentRecordRDD-method.Rd
Writing sortReadsByReferencePositionAndIndex-AlignmentRecordRDD-method.Rd
Writing markDuplicates-AlignmentRecordRDD-method.Rd
Writing recalibrateBaseQualities-AlignmentRecordRDD-VariantRDD-character-method.Rd
Writing realignIndels-AlignmentRecordRDD-method.Rd
Writing save-CoverageRDD-character-method.Rd
Writing collapse-CoverageRDD-method.Rd
Writing toFeatures-CoverageRDD-method.Rd
Writing coverage-CoverageRDD-method.Rd
Writing flatten-CoverageRDD-method.Rd
Writing save-FeatureRDD-character-method.Rd
Writing toCoverage-FeatureRDD-method.Rd
Writing toReads-FragmentRDD-method.Rd
Writing markDuplicates-FragmentRDD-method.Rd
Writing save-FragmentRDD-character-method.Rd
Writing saveAsParquet-GenotypeRDD-character-method.Rd
Writing toVariants-GenotypeRDD-method.Rd
Writing toVariantContexts-GenotypeRDD-method.Rd
Writing save-NucleotideContigFragmentRDD-character-method.Rd
Writing flankAdjacentFragments-NucleotideContigFragmentRDD-numeric-method.Rd
Writing saveAsParquet-VariantRDD-character-method.Rd
Writing toVariantContexts-VariantRDD-method.Rd
Writing saveAsVcf-VariantContextRDD-character-method.Rd
>
>
Warning message:
roxygen2 requires Encoding: UTF-8
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-r) @ adam-r-spark2_2.11 ---
* checking for file ‘bdgenomics.adam/DESCRIPTION’ ... OK
* preparing ‘bdgenomics.adam’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘bdgenomics.adam_0.24.0.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘bdgenomics.adam/man/rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd’
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘bdgenomics.adam/man/rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd’

[INFO]
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-r-spark2_2.11 ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ adam-r-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/heuermh/working/adam-upstream/adam-r/src/test/resources
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-r-spark2_2.11 ---
[INFO] No sources to compile
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (test-r) @ adam-r-spark2_2.11 ---
* using log directory ‘adam/adam-r/bdgenomics.adam.Rcheck’
* using R version 3.5.1 (2018-07-02)
* using platform: x86_64-apple-darwin16.7.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘bdgenomics.adam/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bdgenomics.adam’ version ‘0.24.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  bdgenomics.adam/man/rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd
  bdgenomics.adam/man/rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bdgenomics.adam’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Checking should be performed on sources prepared by ‘R CMD build’.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Duplicated \argument entries in documentation object 'GenomicDataset':
  ‘...’ ‘genomicRdd’ ‘...’ ‘genomicRdd’ ‘...’ ‘genomicRdd’ ‘...’
  ‘genomicRdd’ ‘...’ ‘genomicRdd’ ‘...’ ‘genomicRdd’ ‘...’ ‘genomicRdd’
  ‘...’ ‘genomicRdd’ ‘...’ ‘genomicRdd’ ‘...’ ‘genomicRdd’ ‘...’

Undocumented arguments in documentation object 'toVariants,GenotypeRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'toVariants'
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  4: newJObject(x, ...)
  5: invokeJava(isStatic = TRUE, className, methodName = "<init>", ...)
  6: handleErrors(returnStatus, conn)
  7: stop(readString(conn))

  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 5
  1. Error: (unknown) (@test_adamContext.R#23)
  2. Error: (unknown) (@test_alignmentRecordRdd.R#22)
  3. Error: (unknown) (@test_featureRdd.R#22)
  4. Error: (unknown) (@test_genotypeRdd.R#22)
  5. Error: (unknown) (@test_variantRdd.R#22)

  Error: testthat unit tests failed
  Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘adam/adam-r/bdgenomics.adam.Rcheck/00check.log’
for details.

[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)

@heuermh
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heuermh commented Nov 13, 2018

Got it, needed to re-export SPARKR_SUBMIT_ARGS

...
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘adam/adam-r/bdgenomics.adam.Rcheck/00check.log’
for details.


[INFO]
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-r-spark2_2.11 ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-surefire-plugin:2.22.1:test (default-test) @ adam-r-spark2_2.11 ---
[INFO] No tests to run.
[INFO]
[INFO] --- maven-jar-plugin:3.1.0:jar (default-jar) @ adam-r-spark2_2.11 ---
[WARNING] JAR will be empty - no content was marked for inclusion!
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  01:04 min
[INFO] Finished at: 2018-11-13T16:31:20-06:00
[INFO] ------------------------------------------------------------------------

adam-r (HEAD detached at adam-parent-spark2_2.11-0.25.0)!
$ R CMD build bdgenomics.adam
* checking for file ‘bdgenomics.adam/DESCRIPTION’ ... OK
* preparing ‘bdgenomics.adam’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘bdgenomics.adam_0.25.0.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘bdgenomics.adam/man/rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd’
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘bdgenomics.adam/man/rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd’

This was referenced Nov 13, 2018
Closed
Merged
@heuermh
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heuermh commented Dec 5, 2018

Fixed by #2090

@heuermh heuermh closed this as completed Dec 5, 2018
@heuermh heuermh added this to the 0.26.0 milestone Dec 5, 2018
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