Closed ch4rr0 closed 4 years ago
Hi @ch4rr0
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: snapcount
Type: Package
Title: R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
Version: 0.99.0
Author: Rone Charles
Maintainer: Rone Charles <rcharle8@jh.edu>
Description: snapcount is a client interface to the Snaptron webservices
which support querying by gene name or genomic region.
Results include raw expression counts derived from alignment of RNA-seq samples
and/or various summarized measures of expression across one or more regions/genes
per-sample (e.g. percent spliced in).
Depends:
R (>= 3.2.0)
Imports:
R6,
httr,
rlang,
purrr,
jsonlite,
assertthat,
data.table,
Matrix,
magrittr,
stringr,
stats,
IRanges,
GenomicRanges,
SummarizedExperiment
Suggests:
BiocManager,
bit64,
covr,
knitcitations,
knitr (>= 1.6),
JunctionSeq,
devtools,
BiocStyle (>= 2.5.19),
rmarkdown (>= 0.9.5),
testthat (>= 2.1.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Roxygen: list(markdown = TRUE, roclets = c("rd", "namespace", "collate"))
URL: https://github.com/langmead-lab/snapcount
BugReports: https://github.com/langmead-lab/snapcount/issues
biocViews: Coverage, GeneExpression, RNASeq, Sequencing, Software, DataImport
VignetteBuilder: knitr
ByteCompile: true
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Received a valid push; starting a build. Commits are:
f4bd00f Update travis url
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Received a valid push; starting a build. Commits are:
ce6b817 Remove file in License field and import "is" funct...
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.
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Received a valid push; starting a build. Commits are:
e58a506 Add methods to Imports list
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.
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.
Received a valid push; starting a build. Commits are:
f4d09f2 Update R base version to 4.0 to get suppress warni...
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.
@hpages -- The project now compiles without warning or error and would love to continue the review process.
Hi @ch4rr0 ,
Happy New Year and sorry for the delay.
Looks like the snapcount package is using reference classes. Any reason for that? Bioconductor strongly recommends the use of traditional S4 classes, unless you have a good reason for using something else.
In any case, Bioconductor users are not necessarily familiar with the sb$query_jx()
syntax and should not be required to learn it in order to use your package. Please make sure that your objects support the standard query_jx(sb)
syntax, even if they are reference objects (reference objects also support it), and stick to this syntax in all your examples and vignette.
Thanks! H.
I am working on this.
Any progress on this? Thanks
Still working on the changes. Some additional suggestion were brought during an internal review, so working on addressing those as well.
I will be resubmitting the package tomorrow. Apologies for the delay.
No problem. Thanks for the update.
FYI -- I need to fix some test failures caused by recent changes, so will be delayed by a day.
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.
Received a valid push; starting a build. Commits are:
1036202 Replace is with class and bump version
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.
Received a valid push; starting a build. Commits are:
186ab3e Fix bioductor warnings and bump version
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.
@hpages -- package is ready for review now.
@hpages -- do you think we will be ready for the next bioconductor release?
any updates?
Hi @ch4rr0 ,
Sorry again for the delay.
My major concern remains: the package is still using reference classes. Sorry to ask again but are there any reasons for that? See my comment from Jan 9 above in this issue, and also, if the use of reference classes is really necessary, my recommendation to avoid exposing the end user to things like sb$compilation("gtex")$regions("CD99")$query_jx()
.
Other minor things:
Please address the R CMD check
NOTEs about the LICENSE
file.
Using URLs like
https://bioconductor.org/packages/release/bioc/vignettes/recount/inst/doc/recount-quickstart.html
https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html
is fragile because these URLs are not guaranteed to work in the future. It's much better to use the "canonical URL" for a Bioconductor package (sometimes called the Package Short Url). The canonical URL is of the form: https://bioconductor.org/packages/pkgname
. The Bioconductor project is committed to keep these URLs valid for as long as the project will live.
In ?Compilation
:
If the package cannot connect to the internet the variants will default to:
but there is nothing after "to:"
Too many typos e.g. SnaptonQueryBuilder ("r" missing), RangeSummarizedExperiment ("d" missing), etc... Please re-read carefully your man pages and the vignette.
Thanks, H.
The reference class makes it easy to implement the Builder pattern used in SnaptronQueryBuilder class. We kept it documented, but also provided wrapper functions for users not familiar with R6. I made an attempt to replace all examples outside of the SnaptonQueryBuilder man page with wrapper functions.
I am working on fixing the remaining issues.
FYI -- we are almost done with the changes.
Received a valid push; starting a build. Commits are:
289d748 Bump version
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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.
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Your package has been built on Linux, Mac, and Windows.
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There seems to be an issue with the build bot.
Received a valid push; starting a build. Commits are:
f1bfa2d Bump version to retrigger build
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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: "ABNORMAL". 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.
We're currently looking into this. Thanks!
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.
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.
Thanks for all the improvements to the package. It's in a much better shape. I like that the user can now operate on the SnaptronQueryBuilder objects using the classic R syntax. Note that you still have a few occurrences of "SnaptonQueryBuilder" (the "r" is missing) but that is not a showstopper (you can fix them now or after the package is added to our git server at git.bioconductor.org).
I'm accepting the package.
Cheers, H.
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.
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