Onassis package

[eugeniaeueu]

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• Repository: https://github.com/eugeniaeueu/Onassis

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[bioc-issue-bot]

Hi @eugeniaeueu

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: Onassis
Version: 0.98.0
Date: 2017-05-10
Title: OnASSIs Ontology Annotation and Semantic SImilarity software
Author: Eugenia Galeota
Authors@R: person("Eugenia", "Galeota", email="eugenia.galeota@gmail.com",
  role=c("aut", "cre"))
Maintainer: Eugenia Galeota <eugenia.galeota@gmail.com>
Description: A package that allows the annotation of text with ontology terms
    and the computation of semantic similarity measures between different annotated
    samples.
Depends:
    R (>= 3.3), rJava
Imports:
    GEOmetadb, RSQLite, SRAdb, data.table, methods, tools, utils 
SystemRequirements: Java (>= 1.8)
RoxygenNote: 6.0.1
VignetteBuilder: rmarkdown
Suggests: BiocStyle, knitr, rmarkdown, DT, htmltools
Encoding: UTF-8
LazyData: yes
biocViews: Annotation, DataImport, Clustering, Network, Software, GeneTarget

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Onassis_buildreport_20170510124150.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

6571488 Changed version to trigger the build

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Onassis_buildreport_20170511101730.html

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Onassis_buildreport_20170511120807.html

[lshep]

Hello, Thank you for your submission. Since you have submitted your package for review, we have implemented our MAC builder; I am going to manually kick off a new build to have that information in the report as well. I will review the package and leave feedback in the next few days.

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Onassis_buildreport_20170517074018.html

[lshep]

Can you please investigate this ERROR? I am unable to build or install a local version of your package as well.

[eugeniaeueu]

Hi, I'm trying to solve the issues. The former ones were only on windows platforms and they were arising from the java libraries I am importing from sourceforge. I am compiling them again on Windows and checking if they still work in os and linux.

[lshep]

Is there a reason you aren't bundling the java libraries with the package?

[eugeniaeueu]

I want to add the java libraries in the extdata of the package. Since they are large 85 mb I thought to put them already compiled on sourceforge and download them when the package is installed as extdata. The solution worked on my Os X but doesn't work in windows. I temporally changed the code to show the java classpath during the BUILD. I'm going to trigger a new build. Have you got any hint ? Thanks

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

dcb3c49 OnLoad method changed to show libPaths and java cl...

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Onassis_buildreport_20170518065752.html

[eugeniaeueu]

Hi, this is the report from the latest commit

http://bioconductor.org/spb_reports/Onassis_buildreport_20170518065752.html and the problem is again with windows. I tried to add the jar file to the java classpath in a R console with the following commands having the jar in the current working directory library(rJava) .jinit() .jaddClassPath("C:/Users/defaultUser/Downloads/similarity-0.0.1-SNAPSHOT-jar-with-dependencies.jar") .jnew("iit.comp.epigen.nlp.similarity.Similarity")

In this case the class is created, but I really don't understand what goes wrong with the initJavaLibs method in Onassis

[mtmorgan]

Hi @eugeniaeueu -- I've taken over the review from Lori, to help navigate this issue.

I think first we're reluctant to rely on large jar downloads from 'third party' sites. There are several issues.

1. Bioconductor is supposed to be 'open source', but since only the jar files are available it's not straight-forward for users to discover the underlying code.
2. Redistributing software generally requires conformance to the license of the underlying software, but there is no license on the jar files.
3. using a third-party resource (in this case sourceforge) is not ideal, partly because Bioconductor tries to provide users with a reproducible environment ('normal' Bioconductor packages are available in our SVN repository 'forever') but we cannot guarantee the long-term availability of the sourceforge resource.
4. A second concern with third-party resources is the cost to our build system of downloading the resource on a nightly basis -- packages are built 'fresh' each night, so the build system would pay this price each night.

To work through these, I think

1. The java source code needs to be available, preferably in a versioned (e.g., github) repository.
2. The license for the java code needs to be clearly determined, and of course your redistribution allowed by the license and appropriately acknowledged in the package.
3. Ideally, the java source code and / or jar files would be incorporated into your package or an 'experiment data' package. Likely the java files contain a great deal of infrastructure that is not relevant to their use in R, and they would be trimmed as appropriate.
4. After these hurdles are addressed, we might focus on the specifics of how the jar files are managed; [BiocFileCache][] would be a better solution (using a directory in the installed package directory does not work, because packages are often installed under an 'administrator' account and the installed package directory is not writable by end users).

Let me know what your thoughts are.

[eugeniaeueu]

Dear Martin, thank you for your kind help, For 1 and 2 Regarding the Java source code, I simply compiled with maven a jar including dependencies from the already available repository at https://github.com/UCDenver-ccp/ccp-nlp. This is their license https://github.com/UCDenver-ccp/ccp-nlp/blob/master/LICENSE For the semantic similarity part I modified some source code files, created a new class and compiled the other jar with dependencies from this other repository https://github.com/sharispe/slib. The license in this case is a CeciLL one. Should I fork both the repositories in my github, update the second one with my modifications, copy the license files and then add this information in the DESCRIPTION file of the Onassis repository? Should I also change the License field in the DESCRIPTION file of the Onassis package?

Concerning 3, I already tried to remove some of the infrastructure that is not relevant but the dependencies are so intricate that it's impossible to make the library work without any of the modules. Anyway, I'll give it a try again. I thought that it wasn't possible to create an experiment data for java and jar files, but I can create it and upload it in github.
I'll also give a look at the BiocFileCache. I look forword to hear from you soon. Thanks again,

Eugenia

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

984adda Updated many methods and vignette

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Onassis_buildreport_20170613073532.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

3fd1b65 New version 0.99.5

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Onassis_buildreport_20170614055244.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

605aea7 Changed vignette and DESCRIPTION

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Onassis_buildreport_20170614101008.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

3a2320f Changed CMopts function to automatically set optio...

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Onassis_buildreport_20170622053058.html

[mtmorgan]

Thanks for the submission. Sorry for the slow reply. I won't make any comments on OnassisJavaLibs; t seems fine as it is. When the issues below are addressed, please post a brief summary of the changes you have made.

DESCRIPTION

• Good

vignette

• Good

R

• Validity methods should return text describing errors, rather than stopping. So for instance

  setClass(
      Class = "CMoptions", 
      representation(arguments = "list"),
      validity = function(object) {
          text <- character()
          ...
          if (class(object@arguments) != "list") {
              text <- c(text, "Invalid arguments: Arguments should be a list")
          ...
          if (length(text)) text else TRUE
      }
  )

• Consider constructors CMdictionary <- ... instead of direct calls to new() to separate 'interface' from 'implementation', a major benefit of object-oriented approaches.

• Likewise, always define and use accessor function e.g., dict_location <- function(x) x@dict_location. The accessor functions do not need to be exported if the slot is not meant to be accessed by the user.

• use inherits() (S3) or is() (S4) rather than class().

• Consider formatting code to standard 80 character width, e.g,. using package formatR.

• for generics with multiple arguments, consider using signature= to limit dispatch to the arguments for which dispatch is actually required. This simplifies reasoning about code -- only one alternative path, rather than multiple, required.

• Consider using loadNamespace() rather than library() (CMdict-methods.R:153)

• eval(parse(text=...)) CMdict-methods.R:155 can usually be avoided; I think you want org <- loadNamespace(inputFileOrDb); org[[inputFileOrDb]]

• message() doesn't need paste0() inside -- it pastes args.

man

• good

NEWS

• format so parsed by utils::news()

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

ef2c500 Software updated to meet Bioconductor requirements

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Onassis_buildreport_20170713085949.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

43f1a0c including untracked files 633e55e including untracked files

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Onassis_buildreport_20170713091639.html

[mtmorgan]

have you finished revisions in response to the initial review?

[eugeniaeueu]

Yea, I made all the corrections

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor svn repository and nightly builds. Additional information will be sent to the maintainer email address in the next several days.

Thank you for contributing to Bioconductor!