Discordant R Package Try #2 #178

siskac · 2016-10-23T17:59:13Z

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Repository: https://github.com/siskac/discordant

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bioc-issue-bot · 2016-10-23T17:59:13Z

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 · 2016-10-23T21:14:12Z

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 · 2016-10-23T21:17:51Z

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 · 2016-11-03T20:38:23Z

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

Checking native routine registration...
- WARNING: Register native routines! see
  http://cran.r-project.org/doc/manuals/R-exts.html#Registering-native-routines
Checking for bioc-devel mailing list subscription...
- ERROR: Maintainer should subscribe to the bioc-devel mailing
  list. Subscribe here:
  https://stat.ethz.ch/mailman/listinfo/bioc-devel
Checking man pages...
- WARNING: Add non-empty \value sections to the following man
  pages:
  fishersTrans.Rd, TCGA_Breast_miRNASeq.Rd,
  TCGA_Breast_miRNASeq_voom.Rd, TCGA_Breast_RNASeq.Rd,
  TCGA_Breast_RNASeq_voom.Rd, TCGA_GBM_miRNA_microarray.Rd,
  TCGA_GBM_transcript_microarray.Rd

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 · 2016-11-16T03:33:49Z

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

Valerie

siskac · 2016-11-16T03:35:37Z

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 #178 (comment), or mute the thread https://github.com/notifications/unsubscribe-auth/AI73aTFpTpEpFhIt4RmHx0EZj67Vx8Ysks5q-nmdgaJpZM4KeMmx.

siskac · 2016-11-21T21:48:34Z

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 #178 (comment), or mute the thread https://github.com/notifications/unsubscribe-auth/AI73aTFpTpEpFhIt4RmHx0EZj67Vx8Ysks5q-nmdgaJpZM4KeMmx.

vobencha · 2016-11-21T22:35:00Z

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

siskac · 2016-11-21T23:55:51Z

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?

—
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vobencha · 2016-11-22T01:09:04Z

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 · 2016-11-22T19:00:15Z

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

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vobencha · 2016-11-23T21:54:46Z

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 · 2016-11-29T14:32:00Z

Can you please bump the version?

siskac · 2016-11-29T17:46:09Z

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 ***@***.***> wrote: Can you please bump the version? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#178 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AI73aVDEs4GnSRz_4kHt9B9bmChw7_3zks5rDDdggaJpZM4KeMmx>.

siskac · 2016-12-07T20:48:11Z

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 ***@***.***> 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 ***@***.*** ***@***.***>> wrote: > > Can you please bump the version? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub <#178 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AI73aVDEs4GnSRz_4kHt9B9bmChw7_3zks5rDDdggaJpZM4KeMmx>. >

vobencha · 2016-12-07T20:58:31Z

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

bioc-issue-bot · 2016-12-08T12:02:20Z

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 · 2016-12-08T21:22:10Z

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 · 2016-12-08T21:44:37Z

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

siskac · 2016-12-08T23:35:55Z

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 ***@***.***> 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 <#178 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AI73aRaBUWT23bg0zIbVE28mwMlQHjMVks5rGHpFgaJpZM4KeMmx>.

bioc-issue-bot · 2016-12-09T23:10:52Z

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

5dd0e6e bumped version to 0.99.2 try 2

bioc-issue-bot · 2016-12-09T23:13:29Z

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 · 2016-12-09T23:31:53Z

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

bioc-issue-bot · 2016-12-11T20:40:22Z

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 · 2016-12-11T20:42:11Z

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 · 2016-12-11T20:47:48Z

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 · 2016-12-12T15:03:32Z

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.

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

'mat' argument in split.MADOutlier()
'x' and 'y' arguments in createVectores() and discordantRun()

\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

\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().

\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.

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.

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

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 · 2016-12-19T03:09:33Z

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 · 2016-12-19T03:14:32Z

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 · 2016-12-29T14:07:15Z

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

siskac · 2016-12-29T14:31:08Z

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 ***@***.***> 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 · 2016-12-29T16:36:00Z

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 · 2017-01-02T23:45:04Z

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 · 2017-01-02T23:46:28Z

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 · 2017-01-03T00:26:40Z

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

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

bioc-issue-bot · 2017-01-03T00:30:49Z

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 · 2017-01-09T16:19:24Z

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

…

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On Jan 2, 2017, at 5:30 PM, bioc-issue-bot ***@***.***> 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 · 2017-01-09T16:44:23Z

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 · 2017-01-09T16:54:40Z

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

bioc-issue-bot · 2017-01-09T16:57:40Z

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 · 2017-01-09T17:07:26Z

Thanks @lshep !

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

Checking R Version dependency...
- WARNING: Update R version dependency from 3.3 to 3.4.

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

bioc-issue-bot · 2017-01-10T01:52:21Z

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

0a8dd9f changed R dependency

bioc-issue-bot · 2017-01-10T01:55:43Z

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 · 2017-01-10T18:19:38Z

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!

…

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On Jan 9, 2017, at 6:55 PM, bioc-issue-bot ***@***.***> 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 · 2017-01-10T18:30:07Z

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

bioc-issue-bot added the 1. awaiting moderation label Oct 23, 2016

bioc-issue-bot added 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place and removed 1. awaiting moderation labels Oct 23, 2016

bioc-issue-bot assigned vobencha Oct 23, 2016

bioc-issue-bot added the ERROR label Oct 23, 2016

bioc-issue-bot added the WARNINGS label Dec 8, 2016

bioc-issue-bot removed the WARNINGS label Dec 9, 2016

bioc-issue-bot added the WARNINGS label Jan 3, 2017

mmulvahill mentioned this issue Jan 3, 2017

Rmd version of vignette KechrisLab/multiMiR#11

Closed

bioc-issue-bot removed the ERROR label Jan 9, 2017

bioc-issue-bot added OK and removed WARNINGS labels Jan 10, 2017

vobencha added 3a. accepted will be ingested into Bioconductor daily builder for distribution and removed 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place labels Jan 10, 2017

mtmorgan closed this as completed Jan 12, 2017

Discordant R Package Try #2 #178

Discordant R Package Try #2 #178

Comments

siskac commented Oct 23, 2016

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vobencha commented Jan 10, 2017 • edited Loading

vobencha commented Jan 10, 2017 •

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