CaMutQC - Githubissues

Wangxin555 commented 4 months ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/likelet/CaMutQC

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 4 months ago

Hi @Wangxin555

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: CaMutQC
Type: Package
Title: An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations
Version: 0.99.2
Authors@R: c(person(given = "Xin", family = "Wang", 
           role = c("aut", "cre"),
           email = "sylviawang555@gmail.com",
           comment = c(ORCID = "0000-0002-6072-599X")))
Description: CaMutQC is able to filter false positive mutations generated due to 
    technical issues, as well as to select candidate cancer mutations through a 
    series of well-structured functions by labeling mutations with various flags.
    And a detailed and vivid filter report will be offered after completing 
    a whole filtration or selection section. Also, CaMutQC integrates serveral 
    methods and gene panels for Tumor Mutational Burden (TMB) calculation.  
biocViews: Software, QualityControl, GeneTarget
Encoding: UTF-8
LazyData: false
Suggests: 
    knitr,
    rmarkdown
VignetteBuilder: knitr
RoxygenNote: 7.2.3
NeedsCompilation: no
BugReports: https://github.com/likelet/CaMutQC/issues
URL: https://github.com/likelet/CaMutQC
Depends: R (>= 4.0.0)
Imports: 
    ggplot2,
    dplyr,
    org.Hs.eg.db,
    vcfR,
    clusterProfiler,
    stringr,
    DT,
    MesKit,
    maftools,
    data.table,
    utils,
    stats
License: GPL-3

Wangxin555 commented 4 months ago

Hello,

I just made some modifications and the latest version of CaMutQC should be 0.99.3 now.

bioc-issue-bot commented 4 months ago

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

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

bioc-issue-bot commented 4 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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 following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): CaMutQC_0.99.3.tar.gz

Links above 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/CaMutQC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Wangxin555 commented 4 months ago

Update: Solevd!

Hello, @lshep I ran into a problem when pushing to upstream, and don't know what to do:

$ git fetch --all
Fetching origin
Fetching upstream
git@git.bioconductor.org: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: could not fetch upstream

I am sure that I have added public ssh keys to Github, but I don't know why this problem happens. Could you provide any help?

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 844b65ff5934812664c6d3c1932ac48f6e3c0f91

bioc-issue-bot commented 4 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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 following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): CaMutQC_0.99.4.tar.gz

Links above 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/CaMutQC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 67798648c83b96cd5173745d4ae01114d353077b

bioc-issue-bot commented 4 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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 following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): CaMutQC_0.99.5.tar.gz

Links above 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/CaMutQC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c72fba443f1b6a618775632de836429d53a5c2d8

bioc-issue-bot commented 4 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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 following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): CaMutQC_0.99.6.tar.gz

Links above 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/CaMutQC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Wangxin555 commented 4 months ago

Hi, @lshep I have question about the size limitation of Bioc packages. Now there is only one ERROR in the build report, saying Package tarball exceeds the Bioconductor size requirement. But as it shows in the report, the package size is 4984.42 [KiB], which is smaller than 5Mb. So why am I getting this error? Thank you!

bioc-issue-bot commented 3 months ago

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

DarioS commented 3 months ago

CaMutQC provides a comprehensive set of functions for filtering variants. I noted some coding and documentation issues.

The package has widespread use of for loops. Bioconductor expects vapply or mapply.

Inconsistent use of white space around operators. Refer to Use of Space.

TSL=getValue(CSQ_info$TSL),HGVS_OFFSET = getValue(CSQ_info$HGVS_OFFSET),
PHENO = getValue(CSQ_info$PHENO), MINIMISED = '', 
gnomAD_AF = getgnomInfo(CSQ_info, fieldName = "AF"),

User inputs are not checked. Use is(inputData, "c;lass") to check user input data is correct class.
Inconsistent use of camelCase and snake_case naming. Bioconductor requires snakeCase.
A vignette should have an installation section near the top of it. Also, should have BiocStyle. See Vignettes. Also, the vignette shows a series of outputs but there is no interpretation sentence after each output. Explain what each output means, don't just show a result and start a new section without interpreting it.

Panel of Normals filtration only works for human genomes. That seems overly restricted.

else if (!(genomeVersion %in% c('GRCh38', 'GRCh37'))){
    stop('Invaild genome version.')

Duplication of functionality. There is a readBed function but Biocoductor already has a function in rtracklayer to do that.
```
# read and validate bed file / bed data frame or bed rds
readBed <- function(bedVar, bedHeader = FALSE) {
...        ...
```
Similarly, readINFO seems redundant to Bioconductor's VariantAnnotation package for importing VCF files. Please improve,

Wangxin555 commented 3 months ago

Hi @DarioS Thank you for your suggestions, and we are addressing them. I have a few confusions so far:

In the Bioc contribution manual at here, it says Bioc prefers camelCase but not snakeCase, so we should use camelCase right? Also, I often use lowerCamelCase (first word in lower case, first letter of proceeding words is an uppercase letter), is that ok?
Because we now only focus on the quality control of human cancer somatic mutations, we only consider human genomes for PON files, and I just added a message to notice users. We may support more species in the future. Hope this addresses the 6th point you mentioned.
I fail to find a readBed function in package rtracklayer. But despite we have readBed and readInfo functions that might be similar to some functions in other packages, they are inner functions, which means they are not exported and users are not able to access them directly. I think it is ok to keep them for now, but I might be wrong, so please correct me if I am wrong.

Thank you!

DarioS commented 3 months ago

Yes, lowerCamelCase for variables, UpperCamelCase for class definitions. Thanks for clarifying species. See import e.g. import("example.bed"). Avoiding duplication of existing functionality and increasing use of core infrastructure is important.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 223343886c4ed4dcc95343173d499bea4f35186a

bioc-issue-bot commented 3 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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 following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): CaMutQC_0.99.7.tar.gz

Links above 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/CaMutQC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b2d230db64d92316a354ecc2657b97c08676bc93

bioc-issue-bot commented 3 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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 following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): CaMutQC_0.99.8.tar.gz

Links above 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/CaMutQC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 91e7b70434d297f2d7299c6d3cdfe01d0a7b2cbf

Wangxin555 commented 3 months ago

Hi, @DarioS I have addressed the issues you mentioned:

for loops: I replace more than 10 for loops by apply or vapply, and now there are only about 3 loops in the code of this package.
Inconsistent use of white space around operators: I did a thorough code review on CaMutQC and fixed all inconsistences I could find. Please notify if you find some that I haven't fixed.
User inputs are not checked: I added code to check the class of maf at the begining of every filtration function.
Inconsistent use of camelCase and snake_case naming: Now the name of variables and function are all in camelCase.
A vignette should have an installation section near the top of it: The vignette has been updated and changed to BiocStyle.
Duplication of functionality: I read the code of readBed function in other packages and found that there actually are differences between it and the readBed in CaMutQC, for example, the readBed in CaMutQC can read rds files, or bed files with header, which cannot be achieved by other readBed functions. Similar for readInfo, readINFO in CaMutQC enables the extraction of more information. In addition, due to the special structure of CaMutQC and the functions and features it has, relying on other internal functions may lead to issues in future updates. Therefore, I think it is necessary to implement private inner functions like readbed and readINFO in CaMutQC. But still, we are open to suggestions and comments.

Thanks!

bioc-issue-bot commented 3 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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 following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): CaMutQC_0.99.9.tar.gz

Links above 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/CaMutQC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

DarioS commented 3 months ago

Well done.

bioc-issue-bot commented 3 months ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

Wangxin555 commented 3 months ago

Hi, @DarioS Thank you so much for your comments and updates. It is OK now if I update CaMutQC a little by adding some messages for users?

lshep commented 3 months ago

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

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/Wangxin555.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("CaMutQC"). The package 'landing page' will be created at

https://bioconductor.org/packages/CaMutQC

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.

Bioconductor / Contributions

CaMutQC #3312

Update: Solevd!