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SeSAMe #716

Closed zwdzwd closed 6 years ago

zwdzwd commented 6 years ago

Hi, @vobencha , This is the first submission of the data package for sesame. Per our discussion, I closed the previous issue of this package and resubmit the data package here first. I will submit the code package and post my response to your last review once the data package is approved. Thank you for your help!

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bioc-issue-bot commented 6 years ago

Hi @zwdzwd

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: sesameData
Type: Package
Title: Supporting Data for SeSAMe Package
Description: Provides supporting annotation and test data for SeSAMe package.
Version: 0.99.0
Authors@R: c(person("Wanding", "Zhou", role = c("aut","cre"),
   email = "zhouwanding@gmail.com"),
   person("Hui", "Shen", role = c("aut"),
   email = "Hui.Shen@vai.org"),
   person("Timothy", "Triche", role = "ctb"))
License: Artistic-2.0
Depends: R (>= 3.5)
Suggests: GenomicRanges, BiocGenerics, sesame
biocViews: ExperimentData, MicroarrayData, Genome
NeedsCompilation: no
LazyData: TRUE
RoxygenNote: 6.0.1
bioc-issue-bot commented 6 years ago

A reviewer has been assigned to your package Learn What to Expect during the review process.

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 6 years ago

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zwdzwd commented 6 years ago

AdditionalPackage: https://github.com/zwdzwd/sesame

The line "Remotes: zwdzwd/sesameData" is removed so to let the package depend on the data package just submitted. Version number is reset to 0.99.0.

The following contains responses (in italic) to previous review of this package (in another closed thread #685)

  1. vignette
Nice job with the vignette. Please format the code to 80 characters wide to improve readability. I'd also add relevant detail from this conversation to the vignette background: #685 (comment). That would be helpful information for anyone looking to use the package.


Thanks for the suggestion. I formatted the code to 80 characters wide and eliminated the corresponding NOTE from biocCheck. More detailed information including the description from #685 are included (section “Data structure for Signal Intensities” and section “Functionalities”).

  1. BiocParallel
The mc.* functions from the parallel are not supported on Windows with more than one core. Please use the BiocParallel package instead of parallel. BiocParallel is supported across all platforms and builds on the snow and parallel packages; in other words, you aren't loosing functionality by using BiocParallel.


Thank you for suggesting BiocParallel. I replaced mc functions by the bp* functions and have the package import BiocParallel.

  1. Remove sysdata.rda the from R/ directory.


This is removed.

  1. R code files
Please rename your files to more descriptive names. For example, the test.R file contains code for simulating data. Why not call this simulate.R or simulate_data.R?


_I renamed test.R to simulate_data.R. I also checked other names to make sure they are descriptive (e.g., dm.R to differentialmethylation.R) under the same naming convention.

  1. Remove SeSAMeGetExample and getBuiltInData
AFAICT these functions download data for the examples followed by a complicated caching mechanism. Why did you take this approach instead of including small sample datasets in the package?
I would recommend removing these functions and including sample data in the data/ directory. Load the files in examples with the standard data() or load().


These functions existed because the data sesame depended on (the examples were shrunk to smaller sizes but the annotations are still big) was quite large. I entirely agree with you that this is only confusing and limiting users with poor network connection and probably not portable across platforms. Now both functions are removed and their functionalities are replaced with a depended data package (sesameData). Now examples are loaded from either the inst/extdata/ or data/ from the sesameData, following your recommendation.

  1. man pages
The man pages need more detail. In general they don't explain enough about what the function does, the input/output object, number of samples (?), genes (?), cols, rows what type of data, what the data can be used for etc.
These are a few examples lacking detail but I would encourage you to through all of them and add more information.
 meanIntensity makeExampleTinyEPICDataSet makeExampleSeSAMeDataSet readIDATs ...

I went through all the man pages and expanded the details in the man pages.

  1. dontrun on readIDATs man page
Why is the dontrun in the example necessary? This wrapper is sometimes used when an example takes too long to evaluate but this one doesn't even run:

    library(sesame) ssets <- readIDATs(c('data/5775041003_R02C01', 'data/5775041003_R03C01')) Error in illuminaio::readIDAT(paste0(idat.name, "_Grn.idat")) : Unable to find file data/5775041003_R02C01_Grn.idat

Thanks for the suggestion. I removed all the dontrun in the package and replace them with runnable examples now.

  1. Please remove the date field from DESCRIPTION - this quickly becomes stale.


Thanks for the suggestion. The date field is removed.

  1. reference classes
I think using reference classes in the package is probably unnecessary and certainly confusing. Most R users are not familiar with or expecting reference class behavior. Implementation of the 'in.place' argument (default of FALSE) means you have situations where the standard R semantics (copy on change) are preferred over reference semantics. Having both of these behaviors exposed in one package is not a clean design.
A reference class might make sense in a situation where one function performed multiple steps behind the scenes and modified the data (full copy) in each step. However I don't see that scenario in this package. Instead I see each function as an individual step in the analysis at which point the user may want to inspect results and compare with the previous.
If you are concerned about efficiency in managing large data there are several options available in Bioconductor, DelayedArray and derivatives are a place to start. Or maybe you have another reason for implementing reference classes that I have overlooked ... ?
Please consider using standard S4 classes instead of the reference classes.


Thanks for the suggestion. I added the S4 data structure and made substantial changes to have the rest of the code and annotation data work with the new data structure. The original R6 structure is still kept for backward compatibility. A new function is added to transform current R6 data to the new S4 data. Our original implementation has options “in.place” when it was set to TRUE, no full copy is returned in each step. On a second thought, I hope this R6-S4 change stress the “functional” nature of the language and is more consistent with the Bioconductor programming style.

bioc-issue-bot commented 6 years ago

Dear @zwdzwd ,

You (or someone) has already posted that repository to our tracker.

See https://github.com/Bioconductor/Contributions/issues/685

You cannot post the same repository more than once.

If you would like this repository to be linked to issue number: 716, Please contact a Bioconductor Core Member.

zwdzwd commented 6 years ago

Dear @bioc-issue-bot ,

I have previous posted the repository in #685. The old issue was closed and I opened a new issue to allow the addition of a depended data package (sesameData). Please link this repository to #716 .

Thank you very much for the help!

bioc-issue-bot commented 6 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 build report for more details.

lshep commented 6 years ago

sesameData Package:

sesame Package: Thank you for implementing the already suggested changes. Some other notes:

NAMESPACE

R CODE

Thank you for your submission. I think the code is generally in really good shape and on track to be accepted before the April 11th deadline. Please address the above issues in each of the packages and perform the appropriate version bump to have a rebuild of the package. Please also comment back here with further clarification on what has been addressed.

Cheers

bioc-issue-bot commented 6 years ago

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

1a09870 more initial argument checking

bioc-issue-bot commented 6 years ago

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

b29352a expansion to man pages; added make-data.R

zwdzwd commented 6 years ago

Thank you for the thorough review and encouraging comments! Your comments are addressed below, italicized. Changes are reflected in the latest updates. Let me know if I missed anything.

sesameData Package:

Most of the curation data was first submitted to BioC and the original was provided in http://zwdzwd.github.io/InfiniumAnnotation. Although some part of the detail contained in this curation can overlap with existing data package such as IlluminaHumanMethylation450kprobe, our annotation adds critical correction to the official manifest and necessary additional information (such as the probe location on hg38, and cross-hybridization potential evaluation, binarized reference methylation status for a few cell types, pseudo-autosomal probes in sex chromosomes and extension base identity) for the proper functioning of the sesame package. Much content was detailed in our data curation paper (PMID 27924034). Part of the data included in sesameData also provide models we trained for certain sesame functions (such as inferEthnicity etc). My colleague and I were in charge of curating these data. We made some attempt adopting existing packages but either found they do not suit our direct need. I will keep on studying relevant packages and try to utilize more existing standard annotations. But I hope current approach of providing an independent clean version gives the package better performance and make it perhaps less error-prone. Description of the data sources has been added to reflect the novelty of the included data (below).

Thanks for the suggestion. I created a file named make-data.R under inst/scripts/ folder and added details describing how each piece of the data was obtained, the source (sample IDs, GEO IDs) and scripts showing how the data was preprocessed (background subtraction, genome segmentation etc.).

Thanks for the suggestion. I expanded the man pages for the data/*.rda and included the original data source (GEO experiment IDs or the URLs pointing to the raw data). For processed data, I included scripts that produce the data in make-data.R, for example the script to fit the ethnicity/sex inference model and the script to generate the reference methylation status vectors. For some (e.g, leukocyte reference methylation and the reference methylation of other cell types/tissue types), I also included brief description of the rationale behind the data processing in the man page.

sesame Package: Thank you for implementing the already suggested changes. Some other notes: NAMESPACE are all these exports really necessary or are some internal functions that would not be called by the user? Only export functions that would directly be called by the user.

Thanks for the reminder. I double-checked all the exported functions to make sure they represent a direct interface of the package to the user.

R CODE

I agree and I removed redundant cat functions.

Thanks for the suggestion. I went through the entire code base and adopted match.arg in 21 places (mostly for platform and refversion). 24 new stopifnot were added to perform initial check of the function input.

bioc-issue-bot commented 6 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 build report for more details.

bioc-issue-bot commented 6 years ago

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lshep commented 6 years ago

I'm going to manually rerun both packages for builds - it should allow the software package to find the data package -

bioc-issue-bot commented 6 years ago

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

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bioc-issue-bot commented 6 years ago

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lshep commented 6 years ago

The sesame package looks in good shape and I have no further comments regarding the software package.

The sesameData package is still somewhat concerning regarding the size of the package. It contains a lot of data making it very substantial (and possibly time consuming) for a user to download. We highly recommend reformatting to make this an experiment package that utilizes experimenthub. The benefit being the package becomes a light weight as the data will be stored in Amazon S3 buckets and then you and the users can download data as necessary for use. There is a guideline for experimenthub packages found here. Note the R/ section is optional.

It is very similar to what you already have the differences being

  1. The data will be removed from the package and uploaded to our S3 bucket (I will send you credentials to the email you have utilized to reach out to me) - you will have to use git rm to remove the data and possibly clean the repository which I can send instructions if necessary -
  2. Create a inst/extdata/metadata.csv with required fields for each item you upload to S3. To see if all required columns are present you can use ExperimentHubData::makeExperimentHubMetadata("\<pathto>\sesameData") in an R session that will test reading the metadata.csv.
  3. Create R functions that wrap around the downloading of data from experimenthub
  4. Update to depend on experimenthub
  5. Update vignette as necessary

I can assist with any questions you have regarding this as I am Bioconductor team member that currently manages the hubs.

It looks like there was data pertaining to certain experiments (EPIC, HM27, HM450, etc) - You can either upload each individual file to the hub or if generally all these files are needed for analysis you could save those objects pertaining to the particular type in one .rda file to be uploaded to minimize effort - I don't know the specifics of how these files are utilized so this may not be how they are intended and all individual may be necessary -

Cheers, Lori

bioc-issue-bot commented 6 years ago

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

bcf6997 minor, message omitted

bioc-issue-bot commented 6 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 build report for more details.

lshep commented 6 years ago

Hey there - took a quick glance and a few comments and perhaps useful hints

  1. Why are you defining a new environment? I don't think this is necessary

  2. The query function can take multiple arguments, query(eh, c('sesameData', title)) should get a single resource matching an argument exactly

  3. Also this section can be added to a zzz.R so that each hub data object has its own load function

    .onLoad <- function(libname, pkgname) {
fl <- system.file("extdata", "metadata.csv", package=pkgname)
titles <- read.csv(fl, stringsAsFactors=FALSE)$Title
createHubAccessors(pkgname, titles)
}

    If you check out the experimenthub data package HMP16SData it shows this functionality.

  4. We have internal sets to avoid users accidentally downloading the entire hub - if you use setExperimentHubOption(arg="MAX_DOWNLOADS", 25) , it will change the max download to 25 instead of 10 and avoid the ERROR you are seeing.

Cheers

zwdzwd commented 6 years ago

Thank you for the tips @lshep . The reason I defined a new environment is to avoid repeated loading from disk. For example, if a function that loads the data is called again (in fact some function may be repeated many many times), I want it to reuse the data the same function loaded. Is there a better way to do that with just ExperimentHub? That would be great.

zwdzwd commented 6 years ago

Now I get it. I will use .onLoad. I think it suits my need. Thanks for pointing this out!

Edit: I guess I'm still confused. The accessor functions seem to be loading the data from the disk again everytime it's called. Is there a way to keep an internal copy in memory (just as the environment in my implementation) and return the copy every time the accessor function is called? My apology for missing something obvious!

bioc-issue-bot commented 6 years ago

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

3851c7c version bump 0.99.2

bioc-issue-bot commented 6 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 build report for more details.

bioc-issue-bot commented 6 years ago

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

dcc9a0f update to work with sesameData built on Experiment...

bioc-issue-bot commented 6 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 build report for more details.

bioc-issue-bot commented 6 years ago

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

840bbcd update to sex inference Former-commit-id: 9abb5d... 0ae8dff more update to sex inference Former-commit-id: 8... c9b8f9f minor, message omitted Former-commit-id: 61ca78c... 889c0ca update to sex inference Former-commit-id: 5e0781... 63dd157 minor, message omitted Former-commit-id: af98053... 9017127 minor, message omitted Former-commit-id: e3c0332... 1286400 minor, message omitted Former-commit-id: dfed2f1... 13de4b6 bug fix to hm27 normal control Former-commit-id:... 79c91a0 update to man pages Former-commit-id: 324adc1baa... e558f14 update examples Former-commit-id: 0b45033a65e4a1... 72f1453 minor, message omitted Former-commit-id: 4d0f129... 9d1374c more initial argument checking Former-commit-id:... c66a476 minor, message omitted Former-commit-id: 3bc3965... ae99dfc update to work with sesameData built on Experiment... c708749 added total intensity Z-score Former-commit-id: ...

bioc-issue-bot commented 6 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.

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

Dear Package contributor,

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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.

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bioc-issue-bot commented 6 years ago

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

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

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lshep commented 6 years ago

I'm looking at your packages now and will have further feedback but to answer:

"The accessor functions seem to be loading the data from the disk again everytime it's called. Is there a way to keep an internal copy in memory (just as the environment in my implementation) and return the copy every time the accessor function is called?"

The ExperimentHub returns the object so you could assign in a variable or global variable name - is this what you mean?

lshep commented 6 years ago

The version bump required was from me kicking off the builds manually once the SPB switched to using Bioc 3.8 so I removed the tag.

I will have a review for you shortly.

lshep commented 6 years ago

SesameData Package:

BuildReport:

R code: zzz.R

data.R

inst/extdata: Where are these files being utilized? I can find you actually downloading or analyzing the GSM3040017 files in either the data package or the software package. These files should be removed which will also greatly decrease the size of your package. Please do git rm on the GSM3040017 files and http://bioconductor.org/developers/how-to/git/remove-large-data/ and commit changes.

I see that the 4207113116* files are utilized in sesame so these are fine.

Vignette:

Each has its own download function for example:

EPIC.1.LNCaP = EPIC.1.LNCaP()


**Description:**
- [ ] Remove `LazyData: TRUE`. This rarely proves to be a good thing. In our experience it only slows down the loading of packages with large data.

&nbsp;&nbsp;
&nbsp;&nbsp;
&nbsp;&nbsp;
&nbsp;&nbsp;

**Sesame Software:**
Thank you for implementing the other previously suggested improvements from val.  Some minor additional suggestions: 

**README:**
- [ ] [Optional but strongly encouraged] Add a section for installation from Bioconductor - can still include the install_github as a "development" version"

source("https://bioconductor.org/biocLite.R") biocLite("sesame")


**DESCRIPTION:**
- [ ] [Optional but strongly encouraged] Remove `LazyData: TRUE`. This rarely proves to be a good thing. In our experience it only slows down the loading of packages with large data.

**R code:**
- [ ] As you have designed the S4 class,  it would be better to implement getter/setter methods for the object internals and to use those throughtout your code rather than the `@` 
ex. (these would need to be expanded, possibly check for right formatting, maybe
additional arguments depending on struture, but you get the basic idea )

setMethod("IG", "sigSet", function(x){ x@IG }) setReplacementMethod("IG", "sigSet", function(x, value){ x@IG <- value})


&nbsp;&nbsp;
&nbsp;&nbsp;
&nbsp;&nbsp;
&nbsp;&nbsp;

I think the packages are in a very good state and with these minor improvements be close to ready for acceptance.  
Please implement changes and when ready for a re-review initialize a version bump in the DESCRIPTION for new build reports and comment back here with updates. 

Cheers
lshep commented 6 years ago

You might also find this thread interesting: https://support.bioconductor.org/p/108995/#108998

lshep commented 6 years ago

Hi @zwdzwd Just wanted to check it to see how this was coming along?

zwdzwd commented 6 years ago

Thank you for getting the reviews back @lshep . Sorry that I had been swamped by a few other things in the past week (a paper deadline and a travel) and is just getting back to this. I read your review and I concur with most of the things you mentioned. But I’d like to clarify on three comments you raised and hear your opinion before I move forward to commit changes.

  1. [Quetstion/Discussion] I still don't think you would need environment - if you have a separate function for loading vs processing and assign the data to a variable this would be better than reloading or the potential to reload multiple times anyways - And regardless I don't think its doing what you want -

I now think there is perhaps a fundamental difference between how ExperimentHub was designed and how I intended to use it. As the name suggests, ExperimentHub was intended to be used as a source to load test data or experiment data which is supposed to be used by the users directly. For example, a user could load an “experiment” and start to work on it by applying functions that operates on the experiment. But in my case, I intend to use the data as internal data. I do not want to expose the usage of these data to the user. For example, a data can be about the internal design information about a platform, some package function should handle this data loading instead of having the users manually load every internal data and feed to the function (which will always use the data).

I have indeed considered having separate functions for data loading and processing. But it’s surely damaging the function abstraction idea if the loaded data is for internal use. And in fact, it can be tedious too if there are multiple data that needs be used and the user need to load the independently and feed it to the function that process it.

In other words, I guess what I am getting at can be abstracted into the following equally valid implementation:

implementation1: foo1(input_data, internal_data) {actual_work} implementation2: foo2(input_data) {load_internal_data; actual_work}

I prefer to use foo2 implementation for the internal_data since it does the function abstraction better.

[Required] Please remove the suppressMessages(log <- capture.output(     
sesameDataCacheAll()));

Related to the same complication mentioned above, there is an important side issue related to parallel processing: calling foo2 in parallel means calling load_internal_data in parallel. This will lead to malfunctioning when the data was not cached and needs to be fetched from internet, as I previously mentioned the in the ExperimentHub issue. So I decided to have all the data cached to disk at the time when the package is loaded. I know it's not an ideal solution since this violates the purpose of ExperimentHub that should allow data be cached or loaded only upon needs. But it's at least better than seeing the package not functioning in parallel. This explains why I implemented sesameCacheAll() under zzz.R.

You might also find this thread interesting: https://support.bioconductor.org/p/108995/#108998

Interestingly, I actually I find the top response in this thread you forwarded doing exactly the same thing as I was doing in sesameData package, for the same purpose—reducing disk access from ExperimentHub call. The only difference is in the response of the thread, the parent environment is emptyenv() and in my implementation the environment is under the sesameData package namespace.

I hope you see my struggle. I made multiple attempts to incorporate ExperimentHub, balancing my development goal and the design purpose of ExperimentHub. And this may have already been shared by other users who tried to use ExperimentHub for internal data as well. Please let me know your insights/recommendation or if I missed some important solutions.

Thank you,

lshep commented 6 years ago

Yes that makes sense. We just want to make sure there is sound reasoning behind decisions. Please proceed with the other minor changes but this may be left as implemented. Cheers.

bioc-issue-bot commented 6 years ago

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

41331ed version bump 0.99.2 Former-commit-id: 3851c7c65b... e2fac15 removed global environment Former-commit-id: b37... 1540ef5 removed package environment. this will cause issue... bfc1714 minor, message omitted Former-commit-id: 7e42671... 7d5479a recover package environment, discovered to not aff... 97261ed update to sesame Former-commit-id: fbf2a80cb93c9... 8ee28b2 revert BiocParallel ipclock() Former-commit-id: ... 8527d64 removed more idats Former-commit-id: 1221f75d7d3... f932136 removed version bump Former-commit-id: 39151edb3...

bioc-issue-bot commented 6 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 build report for more details.

bioc-issue-bot commented 6 years ago

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

10434d0 version bump to 0.99.3

bioc-issue-bot commented 6 years ago

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

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bioc-issue-bot commented 6 years ago

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

196b397 removed some warning from new biocCheck b8a7b38 added IG methods 79196e2 added getters and setters ae1e825 fix to setter 20f78d8 added ctl getter/setter f4409a9 version bumped to 0.99.3

zwdzwd commented 6 years ago

Thanks so much for the suggestion on these good practices @lshep . I have altered my implementation following your guide:

Thank you @lshep , let me know if you see other improvements.

bioc-issue-bot commented 6 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 build report for more details.

bioc-issue-bot commented 6 years ago

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

mtmorgan commented 6 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/zwdzwd.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

See further instructions at

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for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using biocLite(\"sesameData\"). The package 'landing page' will be created at

https://bioconductor.org/packages/sesameData

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

mtmorgan commented 6 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/zwdzwd.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using biocLite(\"sesame\"). The package 'landing page' will be created at

https://bioconductor.org/packages/sesame

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.