Closed linxy29 closed 1 year ago
Hi @linxy29
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: DCATS
Type: Package
Title: Differential Composition Analysis Transformed by a Similarity matrix
Version: 0.99.0
Authors@R:
person("Xinyi", "Lin", , "linxy29@connect.hku.hk", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-7780-2461"))
Description: Methods to detect the differential composition abundances between
conditions in singel-cell RNA-seq experiments, with or without replicates,
use total cell number or specific reference group as normalization term.
License: GPL (>= 3)
Depends: R (>= 4.1.0), stats
Imports:
MCMCpack,
matrixStats,
robustbase,
aod,
e1071
Suggests:
testthat (>= 3.0.0),
knitr,
Seurat,
SeuratObject,
SeuratData,
tidyverse,
rmarkdown
VignetteBuilder: knitr
RoxygenNote: 7.2.1
biocViews: SingleCell
Encoding: UTF-8
LazyData: true
Config/testthat/edition: 3
A reviewer has been assigned to your package. Learn what to expect during the review process.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.
Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account
This issue was deemed inappropriate for our issue tracker by a member of the Bioconductor team.
This issue tracker is intended only for packages which are being submitted for consideration by Bioconductor.
Any other use of the tracker is not approved. If you feel this designation is in error, please send us email and include the URL of this issue.
This issue will now be closed.
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: "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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/DCATS
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Your package works primarily with Seurat infrastructure. Would your package be able to process data in the SingleCellExperiment data structure?
Yes, this package can also be used to process data in the SingleCellExperiment data structure. The input metrics can be derived from SingleCellExperiment data structure or Seurat object.
package 'SeuratData' is not available for Bioconductor version '3.17'
-- packages depended on or imported must be in CRAN or Bioconductor. Please follow the guidelines.
Thank you for your reminder. 'SeuratData' is not used in the revised version of DCATS.
A reviewer has been assigned to your package. Learn what to expect during the review process.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.
Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/DCATS
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear reviewers,
'DCATS' have been updated to fix errors. Thank you.
Please fix those two errors first.
Hi Jianhong,
I've subscribed to the mailing list, and added examples on the man pages. Please checked the screenshot as follows.
Please push your changes to git.bioconductor.org with a valid version bump to trigger a new build. Helpful instructions were linked in previous comment: https://github.com/Bioconductor/Contributions/issues/2870#issuecomment-1440493503
Received a valid push on git.bioconductor.org; starting a build for commit id: 9c0fef010b276b6105bbed6b6e28aa242fcffcec
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/DCATS
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear reviewer,
'DCATS' have been updated to fix errors. Thank you.
Thank you for submition your package to Bioconductor. The package passed check and build. Let us start from several things that need to be fixed. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please condsider; Important: must be addressed.
Description
field is required.importFrom
instead of import all with import
.
══ Failed tests ════════════════════════════════
── Failure ('test_prior.R:39:3'): whether phi estimation works ────────────
as.numeric(round(phi, 6)) (actual
) not equal to 0.00793 (expected
).
actual
: 0.0088
expected
: 0.0079
[ ] NOTE: no direct slot access with @
or slot()
- accessors implemented and used.
[ ] Important: warning
, message
, stop
instead of cat
and print
outside of show
methods. Please note that NO paste
in message()
, message
, stop
.
[ ] NOTE: ::
is not suggested in source code unless you can make sure all the packages are imported. Some people think it is better to keep ::
. However please note that you need to manully double check the import items when you make any change in the DESCRIPTION file during development. My recommendation is to remove one or two repeats to force the dependency check.
[ ] Important: 1:n
is not suggested in source code. Use seq_along
or seq.int
instead.
[ ] NOTE: Vectorize: for
loops present, try to replace them by *apply
funcitons.
[ ] Important: Remove unused code.
[ ] NOTE: Avoid using '=' for assignment and use '<-' instead
[ ] Important: Please consider to add drop=FALSE/TRUE
to avoid/make sure the reduction of dimension for matrices and arrays. Ignore this if using datatable.
[ ] NOTE: Functional programming: code repetition.
dcats_betabin
and dcats_GLM
[ ] Important: Vignette should use BiocStyle
package for formatting.
[ ] Important: Vignette should have an Introduction section..
[ ] Important: Please include Bioconductor installation instructions using BiocManager.
[ ] Important: Vignette includes sessionInfo()
.
[ ] Note: Vignette includes motivation for submitting to Bioconductor
as part of the abstract/intro of the main vignette.
[ ] Note: Sugguest to remove the sentence The latest version of the DCATS pacakge is 0.99.1.
.
[ ] Important: all files in data folder need documentation for the process of creating.
Dear reviewers,
I followed the guidance in the link, http://contributions.bioconductor.org/git-version-control.html#new-package-workflow, and updated DCATS. The package version is changed. When I rerun the push commend again, I got: Warning: No xauth data; using fake authentication data for X11 forwarding. X11 forwarding request failed on channel 0 Everything up-to-date
But I didn't receive an email with the build report. I guess something went wrong. How could I fix this?
Thank you for your help.
Please make sure you are pushing to git.bioconductor.org and not github. The git.bioconductor.org version is still 0.99.1 and has not been updated since Mar 8. If you continue to have issues please include the commands you ran with the full output including git remotes -v
Dear Ishep,
I still have the issue mentioned above. Following is the output of commends:
Thank you for your help.
what is your OS?
Following is the output I got after typing "cat /etc/os-release" : NAME="CentOS Linux" VERSION="8" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="8" PLATFORM_ID="platform:el8" PRETTY_NAME="CentOS Linux 8" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:8" HOME_URL="https://centos.org/" BUG_REPORT_URL="https://bugs.centos.org/" CENTOS_MANTISBT_PROJECT="CentOS-8" CENTOS_MANTISBT_PROJECT_VERSION="8"
So I think the Xauth is unique to your system since we have never seen it before. I just googled and there are a few different threads you can look at for debugging -- perhaps this from stackoverflow.
As far as pushing to git.bioconductor.org upstream. I noticed your default branch on github is master? If your default local repo branch is master than you may have to do something like git push upstream master:devel
Dear Ishep,
I tried the solution in the link from StackOverflow. They didn't work. So I tried to push the changes from another server. This time I got the following error message when running "git push upstream devel". Is there any way to solve this error?
error: src refspec devel does not match any error: failed to push some refs to 'git.bioconductor.org:packages/DCATS.git'
When I run "git remote -v", I got:
origin git@github.com:holab-hku/DCATS.git (fetch) origin git@github.com:holab-hku/DCATS.git (push) upstream git@git.bioconductor.org:packages/DCATS.git (fetch) upstream git@git.bioconductor.org:packages/DCATS.git (push)
Is your local branch named something different than "devel" -- like "master" or "main" ? git branch
should show you the name. If so whatever that name is (for example we will say "master") in order to push to devel on git.bioconductor.org you would need to do something like git push upstream master:devel
Did you try:
git checkout devel
git merge origin master # if you need to merge from master
git push upstream devel
Received a valid push on git.bioconductor.org; starting a build for commit id: 1fd9360e74013f787ba2af227bb687202687f6ea
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, skipped". 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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/DCATS
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Thanks @lshep @jianhong, problems solved.
Follwoing is point by point response to the previous review. All important and most of the note were fixed.
Description
field is required.importFrom
instead of import all with import
.[ ] NOTE: no direct slot access with @
or slot()
- accessors implemented and used.
It is hard to find a proper way to replace @
[x] Important: warning
, message
, stop
instead of cat
and print
outside of show
methods. Please note that NO paste
in message()
, message
, stop
.
[x] NOTE: ::
is not suggested in source code unless you can make sure all the packages are imported. Some people think it is better to keep ::
. However please note that you need to manully double check the import items when you make any change in the DESCRIPTION file during development. My recommendation is to remove one or two repeats to force the dependency check.
[x] Important: 1:n
is not suggested in source code. Use seq_along
or seq.int
instead.
[ ] NOTE: Vectorize: for
loops present, try to replace them by *apply
funcitons.
There are multiple steps and variables in for loops. Replacing them by 'apply' fucntion is not easy.
[x] Important: Remove unused code.
[x] NOTE: Avoid using '=' for assignment and use '<-' instead
[x] Important: Please consider to add drop=FALSE/TRUE
to avoid/make sure the reduction of dimension for matrices and arrays. Ignore this if using datatable.
We checked the codes, there are no step leands to the reduction of dimension for matrices
[x] NOTE: Functional programming: code repetition.
BiocStyle
package for formatting.
sessionInfo()
.
motivation for submitting to Bioconductor
as part of the abstract/intro of the main vignette.
The latest version of the DCATS pacakge is 0.99.1.
.Please update the depends to:
Depends: R (>= 4.3.0), stats
It is almost there. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please condsider; Important: must be addressed.
paste
in message()
, message
, stop
1:n
is not suggested in source code. Use seq_along
or seq.int
instead.
Received a valid push on git.bioconductor.org; starting a build for commit id: 2dfd2e0ca1477cd30c59250386152c9e5bffd574
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/DCATS
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear reviewers,
DCATS is revised based on the review comments.
paste
in message()
, message
, stop
1:n
is not suggested in source code. Use seq_along
or seq.int
instead.
File R/detect_reference.R and R/getPhi.R were fixed, there is no 1:n
used in R/svm_simMat.R. The detected one is actually using function svm from the package e1071Please fix the following notes and then I think it is ready to be accepted. There is warning in the biocheck but I can not repeat that. I check the documentation and mark it as false warning.
Code: Note: please condsider; Important: must be addressed.
Received a valid push on git.bioconductor.org; starting a build for commit id: 82d2c76590f43fb4da0703cf386cd4af0a419805
Dear reviewers,
DCATS is revised based on the review comments.
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/DCATS
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@vjcitn Thank you for fix all the comments. I checked the build report, and found that I missed several things:
[ ] Problems with news in NEWS.md: No news entries found. Please add #
in each title line like:
# CHANGES IN VERSION 0.99.3 (2023-04-21)
And make sure update the contents for each updates.
[ ] NOTE: svm_simMat: no visible binding for global variable clusterRes
o Undefined global functions or variables: clusterRes
@lshep Could you please double check about the warning message
* WARNING: Empty or missing \value sections found in man pages.
I must missing something and I can not locate the warning message.
@jianhong Hi jianhong, clusterRes
is one column of an input dataframe. I'm not sure how to address this NOTE.
check function as.formula
, eg
as.formula("clusterRes ~ .")
@jianhong Hi jianhong, I assume the NOTE 'Undefined global functions or variables: clusterRes' means in the svm_simMat
function, there is no defined clusterRes when it is used in the code 'svmfit <- e1071::svm(clusterRes ~ ., data = dataframe[-idxV[[i]],], kernel = "radial")'. But the clusterRes is actually from a input dataframe. It is not defined separately, so I guess this NOTE is not a problem needed to be addressed?
Try my suggestion does not hurt.
Sure, jianhong. Could you specify what you want me to check in function as.formula
, eg as.formula("clusterRes ~ .")
?
line 33 in svm_simMat.R, change
svmfit <- e1071::svm(clusterRes ~ ., data = dataframe[-idxV[[i]],], kernel = "radial")
to
svmfit <- e1071::svm(as.formula("clusterRes ~ ."), data = dataframe[-idxV[[i]],], kernel = "radial")
Dear reviewers,
I failed to trigger a new build again. I used the same code as what I used before. The version of DCATS was changed from 0.99.3 to 0.99.4. My local branch named 'devel'. Following is the output of git remote -v
, git checkout devel
, and git push upstream devel
.
(base) [linxy29@hpc02 DCATS]$ git remote -v origin git@github.com:holab-hku/DCATS.git (fetch) origin git@github.com:holab-hku/DCATS.git (push) upstream git@git.bioconductor.org:packages/DCATS.git (fetch) upstream git@git.bioconductor.org:packages/DCATS.git (push)
(base) [linxy29@hpc02 DCATS]$ git checkout devel Already on 'devel' Your branch is up to date with 'origin/devel'.
(base) [linxy29@hpc02 DCATS]$ git push upstream devel X11 forwarding request failed on channel 0 Everything up-to-date
What should I do in this case? Thank you for your help.
Could you try again with just doing a version bump and show everything from commit to push? Sometime the system gets confused when you do the version bump in a merge and with subsequent commits after. When I do a checkout of your code, the version bump to 0.99.4 was on April 24 but then you had additional commits and pushes without a version bump today.
ie.
git checkout devel
## version bump DESCRIPTION to 1.99.5
git add DESCRIPTION
git commit
git push upstream devel
Received a valid push on git.bioconductor.org; starting a build for commit id: 73f462c2895e223072096819c94eb8f7f1a6c3f0
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/DCATS
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
Confirm the following by editing each check box to '[x]'
[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
[x] I am familiar with the Bioconductor code of conduct and agree to abide by it.
I am familiar with the essential aspects of Bioconductor software management, including:
For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.