HMP16SData

[schifferl]

Hi guys, this is an ExperimentHub package so maybe review should be done by @lshep or @vobencha. Data are there on S3 already and the metadata.csv file has been prepared as well. Will just need to add the resources to production to evaluate the vignette. Both Build and Check pass for me : ) It is a tiny package, can go into release or devel – either is fine. Thanks x 10^6

These commands, to look at the objects quickly without ExperimentHub:

BiocInstaller::biocLite("waldronlab/HMP16SData")
library(HMP16SData)
data("20171011.V13")
data("20171011.V35")
V13
V35

• Repository: https://github.com/waldronlab/HMP16SData

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[bioc-issue-bot]

Hi @schifferl

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: HMP16SData
Type: Package
Title: 16S rRNA Microbiome Data from the Human Microbiome Project
Version: 0.99.0
Author:
    Lucas Schiffer <schiffer.lucas@gmail.com>,
    Rimsha Azhar <rimsha_azhar@hotmail.com>,
    Marcel Ramos <marcel.ramos@roswellpark.org>,
    Ludwig Geistlinger <ludwig.geistlinger@sph.cuny.edu>,
    Levi Waldron <lwaldron.research@gmail.com>
Maintainer: Lucas Schiffer <schiffer.lucas@gmail.com>
Description:
    The HMP16SData package is a Bioconductor ExperimentHub package of the Human 
    Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1-3 
    and 3-5. The raw data files are provided in the package as downloaded from 
    the HMP Data Analysis and Coordination Center website. Processed data is 
    provided as SummarizedExperiment objects via ExperimentHub.
Depends: R (>= 3.4.0)
License: Artistic-2.0
Encoding: UTF-8
LazyData: false
Imports:
    ExperimentHub,
    SummarizedExperiment,
    utils
Suggests:
    Biobase,
    BiocCheck,
    BiocInstaller,
    BiocStyle,
    devtoo,
    dplyr,
    knitr,
    magrittr,
    readr,
    rmarkdown,
    testthat,
    tibble
Remotes: schifferl/devtoo
VignetteBuilder: knitr
URL: https://github.com/waldronlab/HMP16SData
BugReports: https://github.com/waldronlab/HMP16SData/issues
biocViews: Homo_sapiens_Data, ReproducibleResearch, MicrobiomeData
RoxygenNote: 6.0.1

[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/HMP16SData_buildreport_20171016130836.html

[bioc-issue-bot]

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

48a8340 add remotes package to Suggests in DESCRIPTION fil...

[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/HMP16SData_buildreport_20171016151901.html

[bioc-issue-bot]

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

e5c2adb remove devtoo, only used via travis anyway

[bioc-issue-bot]

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

08f7a5d without devtoo, remotes is also removed

[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/HMP16SData_buildreport_20171016152802.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.

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/HMP16SData_buildreport_20171016153139.html

[bioc-issue-bot]

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

8fcf65e remove last of references to devtoo

[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/HMP16SData_buildreport_20171017053029.html

[lshep]

Hey because of the time crunch that today is the deadline for bioc 3.6 it is probably best to go into devel Bioc 3.7 - can you update the BiocVersion in the metadata.csv and I'll get the files into production.

[schifferl]

Great! I will update with the later BiocVersion and then evaluate the vignette once the resources are in production.

[bioc-issue-bot]

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

df4f0e6 Update 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/HMP16SData_buildreport_20171018070845.html

[lshep]

Checking the metadata.csv file:

> library(AnnotationHub)
> temp = readMetadataFromCsv("HMP16SData/")
missing values for 'Coordinate_1_based set to TRUE'
Error in readMetadataFromCsv("HMP16SData/") : 
  RDataPath must start with package name: HMP16SData

Looks like the metadata RDataPath specified uses a lowercase d instead of a capital D: HMP16Sdata/ - could you correct the capitalization please

[bioc-issue-bot]

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

4015267 Update DESCRIPTION

[schifferl]

Thanks @lshep, capitalization issue is resolved.

[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/HMP16SData_buildreport_20171018161901.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.

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/HMP16SData_buildreport_20171019084846.html

[lshep]

HI there,

now that Bioc 3.7 is out the resources are available with the new devel.

Bioconductor version 3.7 (BiocInstaller 1.29.0), ?biocLite for help
> library(ExperimentHub)
> eh = ExperimentHub()
updating metadata: retrieving 1 resource
  |======================================================================| 100%

snapshotDate(): 2017-10-30
> query(eh, "HMP16SData")
ExperimentHub with 2 records
# snapshotDate(): 2017-10-30 
# $dataprovider: NIH Common Fund Human Microbiome Project
# $species: Homo Sapiens
# $rdataclass: SummarizedExperiment
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["EH1037"]]' 

           title
  EH1037 | V13  
  EH1038 | V35  

Please update the vignette, examples, and remove data accordingly and I will take a look at the package.

Note: The single package builder builds will fail as I have not updated the version of Bioconductor they use yet (we normally do this about a week or so after the official release). But I can build and check locally with the understanding that once on our system if any misc ERRORs arise they will need to be fixed asap.

[bioc-issue-bot]

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

ec67db6 changes to satisfy EH requirements :fire:

[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/HMP16SData_buildreport_20171101195517.html

[schifferl]

These errors are related to BBS and annotation packages, will just wait a week or so for things to smooth out and then push a small change to rebuild : )

[bioc-issue-bot]

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

2f87c2d Update 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.

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/HMP16SData_buildreport_20171106104816.html

[schifferl]

@lshep This is ready for a check whenever you want. We can either wait for the SPB version bump or it could be checked locally. The package is passing R CMD check and BiocCheck on Travis CI (https://travis-ci.org/waldronlab/HMP16SData). While that's Linux only, I don't expect different results on macOS or Windows. Many thanks!

[bioc-issue-bot]

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

061c8a3 minor vignette updates

[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/HMP16SData_buildreport_20171106112423.html

[lshep]

Hi Lucas, Sorry for the delay. Looks good and ready to accept. My only comment - You might consider importing all of SummarizedExperiment since your data objects are SummarizedExperiments, once you load the data, you can't explore the objects without manually installing the library (eg. I couldn't do assays(V13) because assays wasn't found).

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git 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!

[mtmorgan]

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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

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(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(\"HMP16SData\"). The package 'landing page' will be created at

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