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Discordant R Package Try #2 #178

Closed siskac closed 7 years ago

siskac commented 7 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Confirm the following by editing each check box to '[x]'

I am familiar with the essential aspects of Bioconductor software management, including:

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

bioc-issue-bot commented 7 years ago

Hi @siskac

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: discordant
Version: 0.99.0
Date: 2016-10-21
Title: The Discordant Method: A Novel Approach for Differential
        Correlation
Authors@R: c(person("Charlotte", "Siska", role = c("aut", "cre"), email = "charlotte.siska@ucdenver.edu"), person("Katerina", "Kechris", role = c("aut")))
Author: Charlotte Siska [cre,aut], Katerina Kechris [aut]
Maintainer: Charlotte Siska <charlotte.siska@ucdenver.edu>
Description: Discordant is a method to determine differential correlation of molecular feature pairs from -omics data using mixture models. Algorithm is explained further in Siska et al.
Encoding: latin1
biocViews: BiologicalQuestion, StatisticalMethod, mRNAMicroarray,
        Microarray, Genetics, RNASeq
Imports: stats, biwt, gtools, MASS, tools
License: GPL (>= 2)
URL: https://github.com/siskac/discordant
NeedsCompilation: yes
Packaged: 2016-10-23 17:49:47 UTC; siskac
bioc-issue-bot commented 7 years ago

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 commented 7 years ago

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/discordant_buildreport_20161023171800.html

vobencha commented 7 years ago

Hi, Please fix these issues raised in the Single Package Builder:

Please remove Discordant_vignette.pdf and discordant_0.99.0.tar.gz from the top level of the package.

Once that's done I'll do a full review.

Valerie

vobencha commented 7 years ago

Checking in. Are you planning to submit an updated version of the package?

Valerie

siskac commented 7 years ago

I’m so sorry, I keep getting hit with deadlines every time I make time to deal with this. I will try to get it done by the end of this week.

Charlotte Siska

On Nov 15, 2016, at 8:33 PM, vobencha notifications@github.com wrote:

Checking in. Are you planning to submit an updated version of the package?

Valerie

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/178#issuecomment-260844503, or mute the thread https://github.com/notifications/unsubscribe-auth/AI73aTFpTpEpFhIt4RmHx0EZj67Vx8Ysks5q-nmdgaJpZM4KeMmx.

siskac commented 7 years ago

Hello Valerie, I’ve made the updates. I did check with Bioccheck, and the same errors are coming up. I registered to Bioconductor, fixed the man pages and pretty sure I registered my C code. Could you please look at it and tell me what to fix? Thanks.

Charlotte Siska

On Nov 15, 2016, at 8:35 PM, Charlotte Siska siskacharlotte@gmail.com wrote:

I’m so sorry, I keep getting hit with deadlines every time I make time to deal with this. I will try to get it done by the end of this week.

Charlotte Siska

On Nov 15, 2016, at 8:33 PM, vobencha <notifications@github.com mailto:notifications@github.com> wrote:

Checking in. Are you planning to submit an updated version of the package?

Valerie

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/178#issuecomment-260844503, or mute the thread https://github.com/notifications/unsubscribe-auth/AI73aTFpTpEpFhIt4RmHx0EZj67Vx8Ysks5q-nmdgaJpZM4KeMmx.

vobencha commented 7 years ago

All of the errors are exactly the same as the last build report?

siskac commented 7 years ago

I see what I did wrong - I got confused where to register, and did it on the mailing list but not the support. Still getting errors about registering native routines, which I thought I did. I followed the instructions given in the link you sent. I had to take out the description of datatypes (REALSXP, INTSXP) because it was causing an error while compiling. Do you have any advice?

Thanks, Charlotte Siska

On Nov 21, 2016, at 3:35 PM, vobencha notifications@github.com wrote:

All of the errors are exactly the same as the last build report?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/178#issuecomment-262089279, or mute the thread https://github.com/notifications/unsubscribe-auth/AI73aSfyccFBLfiZzZ6xEXNKvekD0ezoks5rAhyUgaJpZM4KeMmx.

vobencha commented 7 years ago

No, without seeing the error I can't help. Please bump the version and commit to the master branch. The single package builder will produce another build and I'll see the remaining errors in that output.

For an example of a package that uses C code and registers routines look at GenomicAlignments: svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicAlignments

Valerie

siskac commented 7 years ago

I figured out how to register native routines. Thank you for the help. I just pushed the updated version onto github. Please let me know if you need anything else.

Charlotte Siska

On Nov 21, 2016, at 6:09 PM, vobencha notifications@github.com wrote:

No, without seeing the error I can't help. Please bump the version and commit to the master branch. The single package builder will produce another build and I'll see the remaining errors in that output.

For an example of a package that uses C code and registers routines look at GenomicAlignments: svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicAlignments https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicAlignments Valerie

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/178#issuecomment-262117842, or mute the thread https://github.com/notifications/unsubscribe-auth/AI73afmcc92I2_nEk1_ZJ9s2kb4PT946ks5rAkCxgaJpZM4KeMmx.

vobencha commented 7 years ago

You need to bump the version in your master github branch. This is the trigger for the single package builder. Once that's done we should see a new build report. Valerie

vobencha commented 7 years ago

Can you please bump the version?

siskac commented 7 years ago

I think I just bumped the version. I apologize, I’m new to this and I thought updating the version in the DESCRIPTION file did they trick. Please let me know if it works.

Charlotte Siska

On Nov 29, 2016, at 7:32 AM, vobencha notifications@github.com wrote:

Can you please bump the version?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/178#issuecomment-263585148, or mute the thread https://github.com/notifications/unsubscribe-auth/AI73aVDEs4GnSRz_4kHt9B9bmChw7_3zks5rDDdggaJpZM4KeMmx.

siskac commented 7 years ago

so, I am really confused. I bumped the version, but a new build report was not created? I bumped it on git, was I supposed to do it on svn as well? Any insights would be appreciated.

Charlotte Siska

On Nov 29, 2016, at 10:46 AM, Charlotte Siska siskacharlotte@gmail.com wrote:

I think I just bumped the version. I apologize, I’m new to this and I thought updating the version in the DESCRIPTION file did they trick. Please let me know if it works.

Charlotte Siska

On Nov 29, 2016, at 7:32 AM, vobencha <notifications@github.com mailto:notifications@github.com> wrote:

Can you please bump the version?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/178#issuecomment-263585148, or mute the thread https://github.com/notifications/unsubscribe-auth/AI73aVDEs4GnSRz_4kHt9B9bmChw7_3zks5rDDdggaJpZM4KeMmx.

vobencha commented 7 years ago

It should have been. I'll ask Lori for a forced build.

bioc-issue-bot commented 7 years ago

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/discordant_buildreport_20161208070300.html

siskac commented 7 years ago

I searched the errors on the internet, and I found on the forum this error can happen at random. http://thread.gmane.org/gmane.science.biology.informatics.conductor.devel/9264

Should I do another build? Or is there something I can do to prevent this error in the future?

vobencha commented 7 years ago

You can ignore the MiKTeK errors for now. We see this warning on linux:

You need to remove the inst/doc directory and the build/ directory. Bump the version and resubmit. Valerie

siskac commented 7 years ago

ok I just removed the directories and bumped the version but not seeing any build. is there another step that I am missing? Thanks.

On Dec 8, 2016, at 2:44 PM, vobencha notifications@github.com wrote:

You can ignore the MiKTeK errors for now. We see this warning on linux:

creating vignettes ... OK Warning: inst/doc files Discordant_vignette.Rnw, Discordant_vignette.pdf ignored as vignettes have been rebuilt. You need to remove the inst/doc directory and the build/ directory. Bump the version and resubmit. Valerie

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/178#issuecomment-265864732, or mute the thread https://github.com/notifications/unsubscribe-auth/AI73aRaBUWT23bg0zIbVE28mwMlQHjMVks5rGHpFgaJpZM4KeMmx.

bioc-issue-bot commented 7 years ago

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

5dd0e6e bumped version to 0.99.2 try 2

bioc-issue-bot commented 7 years ago

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/discordant_buildreport_20161209181329.html

vobencha commented 7 years ago

I'm able to reproduce this error on my linux system so it is real, not a problem with the builders:

siskac commented 7 years ago

I realized what happened, i accidentally deleted my .bib file for the vignette. Attempting to fix it now.

charlotte

On Dec 9, 2016, at 4:31 PM, vobencha notifications@github.com wrote:

I'm able to reproduce this error on my linux system so it is real, not a problem with the builders:

creating vignettes ... ERROR Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'Discordant_vignette.tex' failed. BibTeX errors: The top-level auxiliary file: Discordant_vignette.aux The style file: ieeetr.bst I couldn't open database file Discordant_bib_v3.bib ---line 46 of file Discordant_vignette.aux : \bibdata{Discordant_bib_v3 : } I'm skipping whatever remains of this command I found no database files---while reading file Discordant_vignette.aux Calls: -> texi2pdf -> texi2dvi Execution halted — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/178#issuecomment-266152084, or mute the thread https://github.com/notifications/unsubscribe-auth/AI73aRVN_G_ySei1_2P3XAV-_L4zEn0Zks5rGeTqgaJpZM4KeMmx.

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 7 years ago

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

7da8674 bumped 0.99.3 update DESC 44b4ea6 Merge branch 'release-0.99.3'

bioc-issue-bot commented 7 years ago

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/discordant_buildreport_20161209184943.html

bioc-issue-bot commented 7 years ago

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

e75592a Merge branch 'release-0.99.3' into develop 37b33d1 fixed errors, version 0.99.5 51ad63b Merge branch 'release-0.99.5' bb6cb93 updated DESC for 0.99.5 8bd078c Merge branch 'release-0.99.5'

bioc-issue-bot commented 7 years ago

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/discordant_buildreport_20161211154214.html

siskac commented 7 years ago

It seems with latest version 0.99.5 there are no errors in malbec2, but still getting errors about the vignette for tokay2 and oaxaca. Please let me know how I should proceed.

vobencha commented 7 years ago

Hi,

We can ignore the MiKTeK errors on windows and mac for now. I've done the full review and below are some comments and suggestions.

1) Add Depends R (>= 3.4) in DESCRIPTION; all new packages are developed against the devel branch.

2) inputs

Biocondcutor encourages interoperability between packages. If methods in your package support (as input) the base infrastructure classes it's easier for a user to apply your method to their data.

Please have a look at the ExpressionSet, SummarizedExperiment or MultiAssayExperiment classes.

http://www.bioconductor.org/packages/3.5/bioc/html/Biobase.html

http://www.bioconductor.org/packages/3.5/bioc/html/SummarizedExperiment.html

http://www.bioconductor.org/packages/3.5/bioc/html/MultiAssayExperiment.html

One of those should be appropriate as inputs, e.g., please support one of these classes as the

3) \details in man pages

Please add a \details section to these man pages: createVectors.Rd, discordantRun.Rd, fishersTrans.Rd and splitMADOutlier.Rd. Explain a bit about what they do and how they are unique to the package, e.g., a fisher transformation is

4) \value in man pages

The \value section should describe the output object in general and then list specifics. Using split.MADOutlier() as an example,

\value{ \item{mat.filtered}{Input matrix where features with outliers filtered out.} \item{index}{Index of features that have no outliers.} }

If I run the example at the bottom of the page I get a 'mat.filtered' variable. There is no guarantee the use will name this result 'mat.filtered' so it doesn't make sense to document that name in as output in \value. The actual output is a matirx:

class(mat.filtered)

With these dimnames (what do they mean?):

dimnames(mat.filtered) [[1]] [1] "hsa-mir-574"

[[2]] [1] "1" "1.1" "1.2" "1.3" "1.4" "1.5" "1.6" "1.7" "1.8" "1.9" [11] "1.10" "1.11" "1.12" "1.13" "1.14" "2" "2.1" "2.2" "2.3" "2.4" [21] "2.5" "2.6" "2.7" "2.8" "2.9" "2.10" "2.11" "2.12" "2.13" "2.14" [31] "2.15" "2.16" "2.17" "2.18" "2.19" "2.20" "2.21" "2.22" "2.23" "2.24" [41] "2.25" "2.26" "2.27" "2.28" "2.29" "2.30" "2.31" "2.32" "2.33" "2.34" [51] "2.35" "2.36" "2.37" "2.38" "2.39" "2.40" "2.41"

I don't see an 'index' as part of the output so I'm not sure why it's documented in \value. This needs to be fixed in all function man pages not just split.MADOutlier().

5) \arguments section on man pages

On fisherTrans.Rd the 'rhoV' input is described as a integer or numeric list. It's not a list but a vector:

class(rhoV) [1] "numeric" is(rhoV, "list") [1] FALSE

Please double check the object types you've listed for the inputs.

6) dependencies

i) Please remove this from the vignette:

\section{Required packages} R packages WGCNA, gtools, MASS and tools are required.

When the DESCRIPTION and NAMESPACE are properly specificed you don't need to tell the use what packages discordant depends on. When biocLite("discordant") is called, all depedencies are automatically loaded.

ii) You load MASS in the fisherTrans() example for mvrnorm(). This is fine but if you expect the user to need this and other functions from MASS you could put it in 'Depends' in DESCRIPTION. I don't think the MASS package is heavy to load and it may be a good idea to make all those functions available to the user by just loading discordant.

7) Please format your code to a max of 80 characters wide.

8) evaluate vignette code chunks

None of your code chunks are evaluated. Instead they are wrapped in \begin{verbatim}, \end{verbatim}. Please remove the verbatim statements and evaluate the code.

We recommend the use of the BiocStyle pacakge:

http://www.bioconductor.org/packages/3.5/bioc/html/BiocStyle.html

There are vignettes on the package landing page that show how to create a pdf or html vignette.

9) add checks for input values

I would recommend adding some checks in your code to confirm the inputs are what you expect. For example, if I give a 'groups' vector of length 2 to createVectors() no warning or error is thrown and yet the NAs are probably not what was intended. If it's expected that 'groups' is recycled that should be in the documentation.

vectors1 <- createVectors(TCGA_GBM_transcript_microarray, TCGA_GBM_miRNA_microarray, groups = groups)

sapply(vectors1, function(xx) sum(is.na(xx))) v1 v2 0 0

vectors2 <- createVectors(TCGA_GBM_transcript_microarray, TCGA_GBM_miRNA_microarray, groups = groups[1:2])

sapply(vectors2, function(xx) sum(is.na(xx))) v1 v2 0 200

Let me know if you have questions.

Valerie

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

vobencha commented 7 years ago

Checking in. I'd like to finalize the package next week if at all possible. Let me know if you have questions. Valerie

siskac commented 7 years ago

I am just about done with edits you gave, but I am having issues with biocstyle in the vignette. Could you direct me to a r package that has a vignette I could reference? Thanks.

Sent from my iPhone

On Dec 29, 2016, at 7:07 AM, vobencha notifications@github.com wrote:

Checking in. I'd like to finalize the package next week if at all possible. Let me know if you have questions. Valerie

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

vobencha commented 7 years ago

Both GenomicTuples and genoset use BiocStyle,

http://www.bioconductor.org/packages/3.5/bioc/html/GenomicTuples.html http://www.bioconductor.org/packages/3.5/bioc/html/genoset.html

bioc-issue-bot commented 7 years ago

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

7b9a67c Merge branch 'release-0.99.5' into develop f60e485 Merge branch 'release-0.99.5' into develop 526ac77 updated R, vignette and DESC 71e03ac set DESC to 0.99.6 fd50a36 Merge branch 'release-0.99.6' 3666fcb bumped version to 0.99.6 7e5618e R updates a5a3dc3 using ours

bioc-issue-bot commented 7 years ago

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/discordant_buildreport_20170102184627.html

bioc-issue-bot commented 7 years ago

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

6e6350e cleaned up git issues 93242f4 Merge branch 'release-0.99.7'

bioc-issue-bot commented 7 years ago

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/discordant_buildreport_20170102193048.html

siskac commented 7 years ago

Hey, could we please get this evaluated by the end of this week? Thanks!

Sent from my iPhone

On Jan 2, 2017, at 5:30 PM, bioc-issue-bot notifications@github.com wrote:

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/discordant_buildreport_20170102193048.html

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

vobencha commented 7 years ago

Sorry for the delay. I think all of the SPB issues have been fixed and it would be best to get a clean build before approval.

@lshep can you please kick off a new SPB for this issue?

lshep commented 7 years ago

Rerunning now, there should be a new build report posted shortly.

bioc-issue-bot commented 7 years ago

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". 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/discordant_buildreport_20170109115739.html

vobencha commented 7 years ago

Thanks @lshep !

@siskac , the last warning to address is updating the R version,

Once that's done we are good to go. Valerie

bioc-issue-bot commented 7 years ago

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

0a8dd9f changed R dependency

bioc-issue-bot commented 7 years ago

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/discordant_buildreport_20170109205542.html

siskac commented 7 years ago

How soon will the R package be on the website? We have a paper that was just accepted on the extensions and would like to include the link to discordant on bioconductor. Thanks!

Sent from my iPhone

On Jan 9, 2017, at 6:55 PM, bioc-issue-bot notifications@github.com wrote:

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/discordant_buildreport_20170109205542.html

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

vobencha commented 7 years ago

It will probably take a week to post on the web site. In the next few days you'll get an email with svn credentials and instructions.

The package will only be available in devel until the next release in April 2017 after which it's available in both. For your publication you can use this link which will take you to the release page unless the package is only available in devel: http://bioconductor.org/packages/discordant

Valerie