biscuiteerData #1270

jamorrison · 2019-09-26T13:53:24Z

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Repository: https://github.com/trichelab/biscuiteerData

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bioc-issue-bot · 2019-09-26T13:53:25Z

Hi @jamorrison

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: biscuiteerData
Type: Package
Title: Data Package for Biscuiteer
Description: Contains default datasets used by the Bioconductor
   package biscuiteer.
Version: 0.99.0
Date: 2019-09-18
Author: Tim Triche, Jr. [aut, cre], Wanding Zhou [aut], Ben Johnson [aut],
        Jacob Morrison [aut], Lyong Heo [aut]
Maintainer: "Tim Triche, Jr." <tim.triche@gmail.com>
License: GPL-3
Depends: R (>= 3.6.0),
         ExperimentHub
Imports: AnnotationHub,
         utils,
         curl
Suggests: knitr,
biscuiteer
LazyData: true
biocViews: ExperimentHub, ExperimentData, Genome, Homo_sapiens_Data
Encoding: UTF-8
RoxygenNote: 6.1.1
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr

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bioc-issue-bot · 2019-09-26T14:30:38Z

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bioc-issue-bot · 2019-09-26T14:35:25Z

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bioc-issue-bot · 2019-09-26T14:40:36Z

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

c2c0452 Fixing examples/vignettes now that data has been a...
abe9a8a Remove biscuiteer from suggests for the time being
08344e3 Merge pull request #4 from jamorrison/master Corr...

bioc-issue-bot · 2019-09-26T14:56:14Z

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

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bioc-issue-bot · 2019-09-26T15:03:39Z

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

b2c34ed Remove html vignette file for Bioconductor submiss...
5749442 Version bump for Biocondcutor
2122f44 Merge pull request #5 from jamorrison/master Bioc...

bioc-issue-bot · 2019-09-26T15:11:46Z

Dear Package contributor,

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

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jamorrison · 2019-09-26T15:13:42Z

AdditionalPackage: https://github.com/trichelab/biscuiteer

bioc-issue-bot · 2019-09-26T15:13:43Z

Hi @jamorrison,

Starting build on additional package https://github.com/trichelab/biscuiteer.

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

The DESCRIPTION file of this additional package is:

Package: biscuiteer
Type: Package
Title: Convenience Functions for Biscuit
Description: A test harness for bsseq loading of Biscuit output, summarization
         of WGBS data over defined regions and in mappable samples, with or
         without imputation, dropping of mostly-NA rows, age estimates, etc.
Version: 0.99.0
Date: 2019-08-22
Author: Tim Triche, Jr. [aut, cre], Wanding Zhou [aut], Ben Johnson [aut], Jacob Morrison [aut], Lyong Heo [aut]
Maintainer: "Tim Triche, Jr." <tim.triche@gmail.com>
URL: https://github.com/trichelab/biscuiteer
BugReports: https://github.com/trichelab/biscuiteer/issues
License: GPL-3
Depends: R (>= 3.6.0), 
     biscuiteerData,
     bsseq
Imports: readr,
     qualV,
     Matrix, 
     impute,
     HDF5Array,
     S4Vectors, 
     Rsamtools,
     data.table,
     Biobase,
     GenomicRanges,
     BiocGenerics,
     VariantAnnotation,
     DelayedMatrixStats,
     SummarizedExperiment,
     GenomeInfoDb,
     Mus.musculus,
     Homo.sapiens,
     matrixStats,
     QDNAseq,
     dmrseq,
     methods,
     utils,
     gtools
Suggests: DSS, 
      covr,
      knitr,
      rlang,
      scmeth,
      pkgdown, 
      roxygen2,
      testthat,
      QDNAseq.hg19,
      QDNAseq.mm10
biocViews: DataImport, MethylSeq, DNAMethylation
Encoding: UTF-8
RoxygenNote: 6.1.1
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr

jamorrison · 2019-09-26T15:27:25Z

Mentioning @ttriche to look at package.

bioc-issue-bot · 2019-09-26T15:27:39Z

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".
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bioc-issue-bot · 2019-09-26T17:33:00Z

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

a9c2ec4 Making gunzip windows compatible
81a28c1 Merge pull request #21 from jamorrison/feature_bio...

bioc-issue-bot · 2019-09-26T17:55:15Z

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Please see the build report for more details.

jamorrison · 2019-09-30T14:08:26Z

Hi @nturaga biscuiteerData and biscuiteer are ready to be reviewed. Let me know what elements I need to change. Thank you.

lshep · 2019-10-11T14:02:58Z

Sorry for the delay - I will be taking over the review for now - I am currently looking at the packages and will post feedback within the next few hours

lshep · 2019-10-11T17:49:55Z

Thank you for your submission please see initial comments below:

Data package

README

We would recommend still showing Bioconductor installation instructions

NEWS

Please see ?news for formatting. Namely the section headers should be
changes in version x.y.z and not include the package name.

DESCRIPTION

We recommend removing lazyData: true. We have rarely found this useful
and actually have found it can slow installation of packages.

R/man

data.R

Could you include source information in the man files. Along with some
indication of the format of the data. (ie. return type is a GRange object,
etc)

Software package

Build report

Please fix global variable and function NOTES
Please fix coding practice NOTES

README

We would recommend still showing Bioconductor installation instructions

NEWS

Please see ?news for formatting. Namely the section headers should be
changes in version x.y.z and not include the package name.

LICENSE

This file isn't needed since GPL-3 listed in description is distributed
with base R. This should also fix the NOTE in the build report.

test

Remove these and replace with real tests. "tricking" the system with
placeholders is not acceptable.

inst

Include an inst/script directory that describes the source information and
any preprocessing for the data in inst/extdata

Clarification

You still include a lot of data with the package in data and
inst/extdata. Is all this necessary since you uploaded data in the hub?

Vignette

I would suggest shorting to just biscuiteer rather than
biscuiteer_vignette as it is much more intuitive for a user to type
vignette("biscuiteer")

-[ ] section 2.3 while it is quick, it seems like wasted effort to recreate the
object you just did in the previous section. perhaps only create the new second
object to show combining.

the results of getLogitFracMeth should be a GRanges object as it expresses
genomic positioning information. Also the idea that functions should be as
endomorphic as possible is a standard best practice.
Where appropriate (meth, coefs, etc) the objects that make up the result
list of WGBSage should be converted to GRanges.
While you use a show the ERROR when the results from trying to view the
results of bisc.CpGindex should be corrected if possible as I feel most (esp. naive) users
will try to investigate the object by the following:

> bisc.CpGindex
CpGindex with 1 row and 3 columns
    hyper.MCF7_Cunha   hypo.MCF7_Cunha ratio.MCF7_Cunha
           <numeric>         <numeric>        <numeric>
1 0.0690734126984127 0.199261516805161 0.34664702851757
  -------
This object is just a DataFrame that has an idea of where it came from:
Error in as.vector(x, mode = "character") : 
  no method for coercing this S4 class to a vector

R / man

WGVSage.R

As mentioned above objects in results that can be expressed as a GRanges
object should.
Do /should the other parameters be checked for correct input? ie.
stopifnot(is.logical(useENSR)) etc ?

atRegions.R

Output should be converted to GRanges

binCoverage.R

We really don't like seeing FIXME in code. These seem more like
TODOs. (and very good TODOs)
Should there be parameter checking on which, QDNAseq, or readLen?

biscuitMetadata.R

dont call a function two different names. Choose one and export it. you
can reference different alias in the man file without explicitly exporting
functions of different names.

byExtremality.R

convert output to GRanges or GRangeList
remove paste0 in stop call. unnecessary

checkBiscuitBED.R

Might want to expand man page with details on what backing up with hdf5 or
what a sparse matrix is. Or at least include links for more info.
no need to create variable err_message if it is returned right away in a
stop. Just place right in stop call.
remove paste0 from message and stop calls.
despite having an argument for how you compute the values of colSpecs
for readr and colClassses for data.table. Shouldn't only the specified
how be done and stored. Otherwise whats the point of asking?

data.R

Expand on the documentation including source and format information.

extremality.R

We never really like to see FIXME in code. This bug should be fixed
before releasing.

fexpit.R

Will this really be useful to a user and need to be exported?
Why can't this be written in one line and returned?

filterLoci.R

Include argument parameter checking

fixNA.R

sparse seems like a mis-leading entry. TRUE/FALSE both return a matrix
object just a matter of what kind.

flogit.R

Is this really useful to the user to export?

getLogitFracMeth.R

the results of getLogitFracMeth should be a GRanges object as it expresses
genomic positioning information. Also the idea that functions should be as
endomorphic as possible is a standard best practice.
not recommended to have two functions doing the same thing. You can alias different names in the man file but dont export both.

loadHDF5.R

Why is this needed and not just directed to the HDF5Array function when
necessary?

read.biscuit.R

Seems odd that this is the only function that has a . in the name. A dot
typically indicates S3 dispathch which this really isn't. Would recommend
removing and using camelcase instead.
don't create extra variable err_message if it is returned in the next
line. Put the message directly into stop call.
not recommended to have two functions doing the same thing. choose read or
load but don't export both. You can alias different names in the man file but
dont export both.

saveHDF5.R

Why is this needed and not just directed to the HDF5Array function when
necessary?

Please revise the packages according to above. When ready please comment here summarizing the changes. Please also remember to do a version bump to trigger a new build report and ping me in a message indicating you are ready for another review.

Cheers!

jamorrison · 2019-10-11T20:12:10Z

Hi @lshep I wanted to let you know that I started making changes based on the corrections you requested. I will have those done early next week and answer any clarifications at that point.

bioc-issue-bot · 2019-10-17T14:32:03Z

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

1301764 Making changes for Bioconductor review process
ac3cc4c Merge pull request #6 from jamorrison/master Maki...

bioc-issue-bot · 2019-10-17T14:33:08Z

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

56103f6 First stage of Bioconductor review changes
10c6130 Changes for Bioconductor review stage 2
0efb3de Round 3 of Bioconductor review changes
5361c1a Merge pull request #23 from jamorrison/feature_bio...

bioc-issue-bot · 2019-10-17T14:39:59Z

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.

bioc-issue-bot · 2019-10-17T14:54:19Z

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.

jamorrison · 2019-10-17T15:19:41Z

Hi @lshep I have addressed the comments you made in your review. Please see below for responses.

Data package

README

We would recommend still showing Bioconductor installation instructions - added

NEWS

Please see ?news for formatting. Namely the section headers should be
changes in version x.y.z and not include the package name. - reformatted

DESCRIPTION

We recommend removing lazyData: true. We have rarely found this useful
and actually have found it can slow installation of packages. - removed, will keep this in mind for
future package submissions

R/man

data.R

Could you include source information in the man files. Along with some
indication of the format of the data. (ie. return type is a GRange object,
etc) - source information/return type added

Software package

Build report

Please fix global variable and function NOTES - fixed
Please fix coding practice NOTES - fixed

README

We would recommend still showing Bioconductor installation instructions - added

NEWS

Please see ?news for formatting. Namely the section headers should be
changes in version x.y.z and not include the package name. - reformatted

LICENSE

This file isn't needed since GPL-3 listed in description is distributed
with base R. This should also fix the NOTE in the build report. - removed

test

Remove these and replace with real tests. "tricking" the system with
placeholders is not acceptable. - my apologies, I have added one test for the time being and will
add more as the package matures

inst

Include an inst/script directory that describes the source information and
any preprocessing for the data in inst/extdata - directory and scripts added to describe extdata, a
script was also added to show how some of the files in the data directory were created (to go with
the comments on data.R)

Clarification

You still include a lot of data with the package in data and
inst/extdata. Is all this necessary since you uploaded data in the hub? - Some of the final
functionality of biscuiteer is still being worked out, so we are unsure which datasets will be
needed. Once this decision has been made, we will either remove the data entirely, or move it to
the hub.

Vignette

I would suggest shorting to just biscuiteer rather than
biscuiteer_vignette as it is much more intuitive for a user to type
vignette("biscuiteer") - vignette name changed to biscuiteer.Rmd
section 2.3 while it is quick, it seems like wasted effort to recreate the object you just did in
the previous section. perhaps only create the new second object to show combining. - removed
repeat creation of first object
the results of getLogitFracMeth should be a GRanges object as it expresses
genomic positioning information. Also the idea that functions should be as
endomorphic as possible is a standard best practice. - getLogitFracMeth returns a GRanges now
Where appropriate (meth, coefs, etc) the objects that make up the result
list of WGBSage should be converted to GRanges. - Combined meth and coefs into one GRanges
object that is included in the output list
While you use a show the ERROR when the results from trying to view the
results of bisc.CpGindex should be corrected if possible as I feel most (esp. naive) users
will try to investigate the object by the following: - fixed

> bisc.CpGindex
CpGindex with 1 row and 3 columns
    hyper.MCF7_Cunha   hypo.MCF7_Cunha ratio.MCF7_Cunha
           <numeric>         <numeric>        <numeric>
1 0.0690734126984127 0.199261516805161 0.34664702851757
  -------
This object is just a DataFrame that has an idea of where it came from:
Error in as.vector(x, mode = "character") : 
  no method for coercing this S4 class to a vector

R / man

WGBSage.R

As mentioned above objects in results that can be expressed as a GRanges
object should. - see above
Do /should the other parameters be checked for correct input? ie.
stopifnot(is.logical(useENSR)) etc ? - added parameter checks

atRegions.R

Output should be converted to GRanges - output converted

binCoverage.R

We really don't like seeing FIXME in code. These seem more like
TODOs. (and very good TODOs) - changed to TODOs
Should there be parameter checking on which, QDNAseq, or readLen? - added parameter
checks

biscuitMetadata.R

dont call a function two different names. Choose one and export it. you
can reference different alias in the man file without explicitly exporting
functions of different names. - biscuitMetadata is the only exported function now

byExtremality.R

convert output to GRanges or GRangeList - converted
remove paste0 in stop call. unnecessary - removed

checkBiscuitBED.R

Might want to expand man page with details on what backing up with hdf5 or
what a sparse matrix is. Or at least include links for more info. - extra description added
no need to create variable err_message if it is returned right away in a
stop. Just place right in stop call. - moved string into stop call
remove paste0 from message and stop calls. - done
despite having an argument for how you compute the values of colSpecs
for readr and colClassses for data.table. Shouldn't only the specified
how be done and stored. Otherwise whats the point of asking? - now uses how to choose
which values to create

data.R

Expand on the documentation including source and format information. - added source and
return information

extremality.R

We never really like to see FIXME in code. This bug should be fixed
before releasing. - since the DelayedArray functionality is currently experimental, I added an
error message to cover the instance mentioned in the FIXME. When DelayedArray/HDF5-backing
is fully implemented, this will be dealt with properly

fexpit.R

Will this really be useful to a user and need to be exported? - not exported anymore
Why can't this be written in one line and returned? - While it could be written in one line, it
is easier to read and maintain when split over multiple lines.

filterLoci.R

Include argument parameter checking - included

fixNA.R

sparse seems like a mis-leading entry. TRUE/FALSE both return a matrix
object just a matter of what kind. - parameter name changed to sparseMatrix

flogit.R

Is this really useful to the user to export? - not exported anymore

getLogitFracMeth.R

the results of getLogitFracMeth should be a GRanges object as it expresses
genomic positioning information. Also the idea that functions should be as
endomorphic as possible is a standard best practice. - see above
not recommended to have two functions doing the same thing. You can alias different names
in the man file but don't export both. - only getLogitFracMeth is exported now

loadHDF5.R

Why is this needed and not just directed to the HDF5Array function when
necessary? - removed

read.biscuit.R

Seems odd that this is the only function that has a . in the name. A dot
typically indicates S3 dispathch which this really isn't. Would recommend
removing and using camelcase instead. - changed to readBiscuit
don't create extra variable err_message if it is returned in the next
line. Put the message directly into stop call. - moved
not recommended to have two functions doing the same thing. choose read or
load but don't export both. You can alias different names in the man file but
dont export both. - only readBiscuit is exported now

saveHDF5.R

Why is this needed and not just directed to the HDF5Array function when
necessary? - removed

Let me know if you have further requests for changes to be made.

lshep · 2019-10-18T12:34:10Z

Thank you. I have no further comments at this time. I look forward to seeing the future developments of this package as well.
Cheers,

bioc-issue-bot · 2019-10-18T12:34:16Z

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 · 2019-10-21T17:15:51Z

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/jamorrison.keys is not empty), then no further steps are required. Otherwise, do the following:

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 BiocManager::install("biscuiteerData"). The package 'landing page' will be created at

https://bioconductor.org/packages/biscuiteerData

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 · 2019-10-21T17:15:54Z

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/jamorrison.keys is not empty), then no further steps are required. Otherwise, do the following:

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 BiocManager::install("biscuiteer"). The package 'landing page' will be created at

https://bioconductor.org/packages/biscuiteer

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.

bioc-issue-bot added the 1. awaiting moderation label Sep 26, 2019

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 Sep 26, 2019

bioc-issue-bot assigned nturaga Sep 26, 2019

bioc-issue-bot added WARNINGS ERROR labels Sep 26, 2019

bioc-issue-bot removed the ERROR label Sep 26, 2019

bioc-issue-bot added OK and removed WARNINGS labels Sep 26, 2019

bioc-issue-bot added the ERROR label Sep 26, 2019

bioc-issue-bot removed the ERROR label Sep 26, 2019

lshep self-assigned this Oct 7, 2019

jamorrison mentioned this issue Oct 16, 2019

Making changes for Bioconductor review trichelab/biscuiteer#23

Merged

lshep 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 Oct 18, 2019

mtmorgan closed this as completed Oct 21, 2019

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biscuiteerData #1270

biscuiteerData #1270

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mtmorgan commented Oct 21, 2019

biscuiteerData #1270

biscuiteerData #1270

Comments

jamorrison commented Sep 26, 2019

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bioc-issue-bot commented Sep 26, 2019

jamorrison commented Sep 26, 2019

bioc-issue-bot commented Sep 26, 2019

bioc-issue-bot commented Sep 26, 2019

bioc-issue-bot commented Sep 26, 2019

jamorrison commented Sep 30, 2019

lshep commented Oct 11, 2019

lshep commented Oct 11, 2019

Data package

Software package

jamorrison commented Oct 11, 2019

bioc-issue-bot commented Oct 17, 2019

bioc-issue-bot commented Oct 17, 2019

bioc-issue-bot commented Oct 17, 2019

bioc-issue-bot commented Oct 17, 2019

jamorrison commented Oct 17, 2019

Data package

Software package

lshep commented Oct 18, 2019

bioc-issue-bot commented Oct 18, 2019

mtmorgan commented Oct 21, 2019

mtmorgan commented Oct 21, 2019