Closed jhsiao999 closed 4 years ago
Hi @jhsiao999
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:
Encoding: UTF-8
Type: Package
Package: peco
Version: 0.99.0
Date: 2019-09-11
Title: A Supervised Approach for **P**r**e**dicting **c**ell Cycle
Pr**o**gression using scRNA-seq data
Authors@R: c(
person("Chiaowen Joyce","Hsiao", email="joyce.hsiao1@gmail.com",
role=c("aut","cre")),
person("Matthew", "Stephens", email="stephens999@gmail.com", role="aut"),
person("John", "Blischak", email = "jdblischak@gmail.com", role="ctb"),
person("Peter", "Carbonetto", email = "peter.carbonetto@gmail.com",
role="ctb"))
Maintainer: Chiaowen Joyce Hsiao <joyce.hsiao1@gmail.com>
Description: Our approach provides a way to assign continuous cell cycle phase
using scRNA-seq data, and consequently, allows to identify cyclic trend
of gene expression levels along the cell cycle. This package provides method
and training data, which includes scRNA-seq data collected from 6 individual
cell lines of induced pluripotent stem cells (iPSCs), and also continuous cell
cycle phase derived from FUCCI fluorescence imaging data.
URL: https://github.com/jhsiao999/peco
BugReports: https://github.com/jhsiao999/peco/issues
License: GPL (>= 3)
Depends: R (>= 3.5)
Imports:
assertthat,
Biobase,
circular,
conicfit,
doParallel,
foreach,
genlasso,
graphics,
methods,
parallel,
stats
Suggests:
knitr,
rmarkdown
Enhances:
parallel
Remotes:
glmgen/genlasso
biocViews:
Sequencing, RNASeq, GeneExpression, Transcriptomics, SingleCell,
Software, StatisticalMethod, Classification, Visualization
VignetteBuilder: knitr
RoxygenNote: 6.1.1
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.
Please update your package to use the more modern SummarizedExperiment or, given the topic of your package, SingleCellExperiment
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.
@mtmorgan Thank you for the feedbacks. We now use SingleCellExperiment to store our data. All examples have been updated accordingly.
@bioc-issue-bot We've bumped the version to 0.99.3.
Hi ChiaoWen, @jhsiao999 Thank you for your submission. Please see the package review below. If you have any questions, feel free to post them as comments below.
Best, Marcel
Overall, the package seems to use list
s often as function outputs. It is
better to have 'endomorphic' operations that take a SingleCellExperiment
as
input and return one with results whenever possible.
Date
field is not really needed.generic
. The 'generic' property should be
reflected in the implementationget
with data
. Simply use data(sce_sub)
apply(x, 1L, ...)
instead of
do.call(rbind, lapply(seq_len(nrow(x)), ...))
which(coldata$chip_id != "NA18511")
can be coldata$chip_id != "NA18511"
and
you can add !
in the front to get the opposite (instead of ==
)Minor:
1:5
instead of c(1:5)
doParallel
for
/lapply
loopssapply
and use vapply
insteadx["coef"]
vs x[2]
) for subsetting data
whenever possible to avoid mistakes when data changesMinor:
seq_along
instead of seq_len(length(...))
TRUE
in if (plot.it == TRUE)
;
if (plot.it)
should be enoughHi ChiaoWen, @jhsiao999 Please provide an item-by-item response to the review. Otherwise, I'd be forced to close the issue due to inactivity. Thank you. -Marcel
@LiNk-NY Hi Marcel, sorry for the delayed response. I've been working on incorporate the package as a Bioconductor single-cell analysis workflow, so that the main input/output object would be SingleCellExperiment
. I will send a response to the comments later today.
Thanks for the reminder,
Joyce
@LiNk-NY Thank you for the useful suggestions. Please see my reply below. These changes have been incorporated into version v0.99.5. https://github.com/jhsiao999/peco
Hi ChiaoWen, @jhsiao999 Thank you for your submission. Please see the package review below. If you have any questions, feel free to post them as comments below.
Best, Marcel
peco #1248
Overall, the package seems to use
list
s often as function outputs. It is better to have 'endomorphic' operations that take aSingleCellExperiment
as input and return one with results whenever possible. The main functions now outputSingleCellExperiment
object. These includecycle_npreg_outsample
anddata_transform_quantile
.DESCRIPTION
- The
Date
field is not really needed.- Looks good
NAMESPACE
- Avoid tagging functions with
generic
. The 'generic' property should be reflected in the implementation I am not sure how to address this comment. In the current version of NAMESPACE, none of the function is tagged withgeneric
. Please let me know if this is still an issue.vignettes
Please respect the 80 column width limit, it makes it easier to maintain and easier to review The code has been edited accordingly.
Avoid using
get
withdata
. Simply usedata(sce_sub)
Data are now loaded usedata
Consider using a more informative dataset name Dataset names are changed to
model_5genes_predict.rda
,model_5genes_train.rda
,sce_top101genes.rda
andtraining_human.rda
.Use
apply(x, 1L, ...)
instead ofdo.call(rbind, lapply(seq_len(nrow(x)), ...))
Changes have been made accordingly.Avoid converting logical to numeric index. Often the logical index is enough:
which(coldata$chip_id != "NA18511")
can becoldata$chip_id != "NA18511"
and you can add!
in the front to get the opposite (instead of==
) Changes have been made accordingly.Minor:
- Simplify code by using
1:5
instead ofc(1:5)
Changes have been made accordingly.R
Please use a standard 1 or 2 cores as default for functions that use
doParallel
Changes have been made accordingly.Prioritize vectorized operations and try to avoid nested
for
/lapply
loops Changes have been made accordingly.Avoid using
sapply
and usevapply
instead Changes have been made accordingly.Use 'character' indices (e.g.,
x["coef"]
vsx[2]
) for subsetting data whenever possible to avoid mistakes when data changes Changes have been made accordingly.data.R
- Use descriptive names Changes have been made accordingly.
Minor:
Consider using
seq_along
instead ofseq_len(length(...))
Changes have been made accordingly.No need to double evaluate to
TRUE
inif (plot.it == TRUE)
;if (plot.it)
should be enough Changes have been made accordingly.
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.
We are working on updating the SPB builders on R 4.0 and Bioc 3.11 the dependency issues is on our end and we are investigating
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.
The dependency issue on our end has been fixed. These results reflect real ERRORs that should be corrected. Cheers
Hi Joyce ChiaoWen, @jhsiao999 Please follow up on the issues reported on the SPB. Thank you. -M
Thanks @LiNk-NY! I'll look into this error and let you know if I have any questions.
Joyce
Hi Joyce, @jhsiao999 Any updates on the status of the changes? Thanks.
Hi Marcel,
Apologies fo the delay. I am getting to them before the end of the year. Thanks for you patience!
Joyce
On Thu, Dec 19, 2019 at 2:39 PM Marcel Ramos notifications@github.com wrote:
Hi Joyce, @jhsiao999 https://github.com/jhsiao999 Any updates on the status of the changes? Thanks.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1248?email_source=notifications&email_token=ABWB66S6KMJZMIPFCDCEYOTQZPEWDA5CNFSM4IWMSGVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHKWKZQ#issuecomment-567633254, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABWB66SJ55YKXH2XUJEBRULQZPEWDANCNFSM4IWMSGVA .
Hi Marcel @LiNk-NY ,
The errors have been fixed in peco 0.99.6. Please let me know if there are any more issues. Thanks!
Joyce
Hi Joyce, @jhsiao999 Please bump the package's version for another build in the SPB. Thank you. Best, Marcel
Hi Marcel @LiNk-NY ,
I just bumped the version to 0.99.7, made a new build, and pushed the build to the GithHub repo. Thanks!
Joyce
Hi Joyce, @jhsiao999 Thank you for bumping the version. Can you check if the web hook is still active? I don't see a build of your package. CC: @lshep Lori, Is the SPB operational? Thanks.
Hey Marcel @LiNk-NY, I just checked the SPB and everything is running correctly on it.
Hi Marcel @LiNk-NY,
Do you see a build of the package now? I just checked the bioconductor webhook of the repo and it appears to be active (there is also a successful delivery).
P.S. What is the common practice of choosing webhook trigger event? Currently, I select "Just the Push Event". Thanks!
Joyce
Hi Joyce, @jhsiao999
The build message should look like the comment above.
You have the right trigger selected.
Try bumping the package z
version (x.y.z
) again.
@Kayla-Morrell Thanks for looking into it Kayla!
Received a valid push; starting a build. Commits are:
38e78ec trigger bioconductor build
Hi Marcel,
I bumped the version again. The push event seems to have triggered the above message.
Joyce
Hi Joyce, @jhsiao999
The build message should look like the comment above.
You have the right trigger selected. Try bumping the package
z
version (x.y.z
) again.@Kayla-Morrell Thanks for looking into it Kayla!
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.
Received a valid push; starting a build. Commits are:
45dad56 bump to v0.99.9
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.
@LiNk-NY What do you suggest I should do to handle the following warning? Thanks!
Joyce
* Checking R Version dependency...
* WARNING: Update R version dependency from 3.5 to 4.0.
@jhsiao999
Because Bioconductor devel uses R-devel. It is recommended that you
change the R version dependency to 4.0.0
in the DESCRIPTION
file.
Received a valid push; starting a build. Commits are:
ee94ff4 change dependency to R4.0
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.
Hi Joyce, @jhsiao999 I don't see your line-by-line response to the review. I will check the changes today. Best, Marcel
Hi Joyce, @jhsiao999
I now noticed your line-by-line responses. In the future, please add more empty lines between original text and your responses for readability. (See below for an example)
Avoid tagging functions with generic. The 'generic' property should be reflected in the implementation
I am not sure how to address this comment. In the current version of NAMESPACE, none of the function is tagged with generic. Please let me know if this is still an issue.
Some functions such as fit_trendfilter_generic
have the generic
tag in the name.
This should just be a regular function called fit_trendfilter
unless you're creating a
'generic' for which you have and own a class to apply the method to (in S4 the
implementation would involve setGeneric
and setMethod
).
Hi Joyce, @jhsiao999 Any updates?
Hi Marcel @LiNk-NY,
I didn't have time to look into this yet. I'll fix it this weekend. Thank you!
Joyce
Thank you Joyce! @jhsiao999
Hi Joyce, @jhsiao999
It's been a few weekends. Do you have updates to peco
?
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: "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.
Received a valid push; starting a build. Commits are:
2afba13 version bump and README.md update
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.
Received a valid push; starting a build. Commits are:
7f38529 version bump to 0.99.13 and bug fixes
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.
Received a valid push; starting a build. Commits are:
1e79324 version bump to 0.99.14 and fixes to Travis-CI and...
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.
Hi Joyce, @jhsiao999
Thanks for making those changes. Do the packages need a version number dependency?
https://github.com/jhsiao999/peco/blob/1e79324378a8e13b0fd26be8401ce7f6f8f418e9/DESCRIPTION#L26-L37
Usually, you add a version number if there is a feature that is only implemented in a particular version or above. Is that the case for all the packages listed in the DESCRIPTION
file with the exception of R
?
Hi @LiNk-NY,
I cannot be sure of all the specific features that are implemented in a particular version of these pages. The version numbers are added in case of a possible feature that I am not aware of. I usually do this for my R packages to avoid possible versioning issues during software installation. This is probably more of a concern for newer packages such as scater
, SingleCellExperiment
and SummarizedExperiment
.
What do you think about keep the version numbers of the newer packages? Is this acceptable?
Thanks, Joyce
Hi @LiNk-NY,
We have received requests about using our package for R3.6. The current version requires R>=4.0. Any suggestions on how to approach this? For example, could we create a new branch release compatible with R3.6? Would this trigger a new Bioc package built? Thanks!
Joyce
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