Closed BMEngineeR closed 3 years ago
Hi @BMEngineeR
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: IRISFGM
Type: Package
Title: Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq
Version: 0.99.0
Date: 2020-12-22
Author: Yuzhou Chang
Maintainer: Yuzhou Chang <yuzhou.chang@osumc.edu>
Description: Single-cell RNA-Seq data is useful in discovering cell heterogeneity and signature genes in specific cell populations in cancer and other complex diseases. Specifically, the investigation of functional gene modules (FGM) can help to understand gene interactive networks and complex biological processes. QUBIC2 is recognized as one of the most efficient and effective tools for FGM identification from scRNA-Seq data. However, its availability is limited to a C implementation, and its applicative power is affected by only a few downstream analyses functionalities. We developed an R package named IRIS-FGM (integrative scRNA-Seq interpretation system for functional gene module analysis) to support the investigation of FGMs and cell clustering using scRNA-Seq data. Empowered by QUBIC2, IRIS-FGM can identify co-expressed and co-regulated FGMs, predict types/clusters, identify differentially expressed genes, and perform functional enrichment analysis. It is noteworthy that IRIS-FGM also applies Seurat objects that can be easily used in the Seurat vignettes.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.0), MCL, anocva, Polychrome, RColorBrewer, colorspace, AnnotationDbi, ggplot2, org.Hs.eg.db, org.Mm.eg.db, pheatmap, AdaptGauss, DEsingle,DrImpute, Matrix, Seurat, SingleCellExperiment, clusterProfiler, ggpubr, ggraph, igraph, mixtools, scater, scran, stats, methods
LinkingTo: Rcpp
RoxygenNote: 7.1.1
Encoding: UTF-8
Collate:
'Classes.R'
'generics.R'
'AddMeta.R'
'Bicluster.R'
'Bric.R'
'CellTypePrediction.R'
'DifferentialGene.R'
'DimensionReducntionBasedOnLTMG.R'
'EnrichPathway.R'
'InputData.R'
'LTMGSCA.R'
'LTMG.R'
'Object.R'
'PlotHeatmap.R'
'PlotNetwork.R'
'PreprocessData.R'
'RcppExports.R'
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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/IRISFGM
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
@Kayla-Morrell Hi Kayla, thank you in advance for your help with checking the package submission. Regarding the most recent error from the bioc-issue-bot report (.Rproj file), I pushed changes to address these yesterday, but it has not automatically checked it again. Is there something we need to do to have the bioc-bot re-check? The package should be ready to review now that the issue is fixed. Thank you!
@BMEngineeR - Be sure that you are also pushing a version bump with changes, this is what will trigger the new build.
Received a valid push on git.bioconductor.org; starting a build for commit id: 2d18d4d294f2be703e2b72cb9af8b89cb1edbfe0
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/IRISFGM
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 56d7c7d0adb9a133a448ee4cb8ce3f52b2e2bc6f
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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 799a782ed6ecfc63796d97a4b2dd9976f5a9c415
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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
@BMEngineeR - I saw that you made a push yesterday but no build report was posted. I went ahead and kicked off a manual build so you got a build report. The latest build report is a reflection of the latest changes you pushed.
Best, Kayla
@BMEngineeR -
Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.
[x] REQURIED: License 'GPL (>= 2)' is unknown; licenses cannot restrict use. I believe 'GPL-2' would be sufficient here.
[ ] SUGGESTION: I would move 'knitr' from the Imports field to a Suggests field since this package is used to create vignettes. Unless you actually utilize functionality from the package within your code. The Imports is reserved for packages that provide functions, methods, or classes to your package while Suggests are for packages that are used in vignettes, examples, and conditional code.
[ ] SUGGESTION: We strongly encourage the use of the 'BugReports:' field which includes the relevant link to Github for reporting Issues.
utils::news(package="IRISFGM")
.[x] REQUIRED: Only the vignette file (.Rnw or .Rmd) should be present in this directory. Please remove the other files.
[ ] SUGGESTION: I would do a quick read through of the vignette. There are some spelling errors that should be addressed, for example in the heading 'Introduction to IRIS-FGM' Introduction is misspelled and in the heading 'Object structure' Object is misspelled.
[x] REQUIRED: For the section where you talk about pre-installed packages, this code should not be individual inline code but they should all be in a single code chunk. You should show installing packages (minus BiocManager) using BiocManager, not install.packages (BiocManager will work for non-Bioconductor packages as well). You should not be using github to install seurat, this should also be done through BiocManager.
[x] REQUIRED: When showing how to install the IRISFGM package this should be
demonstrated using Bioconductor. The code should look something like the
following and should include eval=FALSE
.
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("IRISFGM")
[x] REQUIRED: All code should be included in code chunks, for example the code you use to demonstrate reading from .h5 file and 10X folder. Instead of inline code this should be a code chunk like you do for setting the directory/importing the library and reading the .csv or .txt file.
[x] REQUIRED: All code chunks need to be evaluated to demonstrate that the
code works without errors. Please be sure code chunks do not include
eval=FALSE
.
[x] REQUIRED: Use accessors; we do not allow for S4 class slots to be accessed via '@' in examples or vignettes (line 239).
[ ] SUGGESTION: For any function that isn't being exported I would suggest
adding the @keywords internal
tag to the documentation. This will remove the
function from the package index. This should definitely be done for any function
that is internal (meaning it starts with a '.') because these functions should
be shown in documentation, they aren't intended to be exposed to the user.
[ ] REQUIRED: Add runnable examples to the following man pages which document exported objects:
[ ] REQUIRED: We require all exported objects to have runnable examples, is there a reason why this one is not run? If it is absolutely necessary we prefer donttest{} instead of dontrun{}.
[x] REQUIRED: Avoid sapply(); use vapply() if possible.
[ ] REQUIRED: Various apply functions should be instead of for loops if possible.
[x] REQUIRED: Avoid 1:...; use seq_len() or seq_along() if possible.
[x] REQUIRED: Avoid the use of direct slot access with '@' or 'slot()'. An accessor method should be created and utilized, especially in functions that are being exported.
[ ] REQUIRED: Is there a reason why you are not exporting the classes defined in your package? If they are to be exported you will need to provide better documentation and information for the slots.
[ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 441 lines that are > 80 characters long.
[ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 305 lines that are not.
Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs.
Best, Kayla
@BMEngineeR - I was wondering if there has been any progress on the points made in my review. We typically like to see changes within a 2-3 week time frame to be sure the package is actively being worked on and it has been just over 3 weeks since I posted my review.
Received a valid push on git.bioconductor.org; starting a build for commit id: 7661554aa10ce671aaab595452fc1ea226406eb8
@Kayla-Morrell Sorry for the concern, I thought the package should be uploaded this Monday. I just reupdate GitHub and re-push to the new version for checking.
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/IRISFGM
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 7a1b957f11898812cd7ac8178d744ff91691eb5e
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/IRISFGM
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 6498aa5dd37958f687c9607a2eca89bfbbc2c7ed
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/IRISFGM
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 207cb23d7a0187d312eece9bb249b7498787adbe
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/IRISFGM
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: a5ee764ad6194861623d81d1c92f7c7b088315b1
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/IRISFGM
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: a625581b436a5e176e105a26e68f3f5831601cc4
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/IRISFGM
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
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