circRNAprofiler - Githubissues

Aufiero commented 5 years ago

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Repository: https://github.com/Aufiero/circRNAprofiler

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bioc-issue-bot commented 5 years ago

Hi @Aufiero

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: circRNAprofiler
Type: Package
Title: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs
Version: 0.1.1
Author: Simona Aufiero
Maintainer: Simona Aufiero <simo.aufiero@gmail.com>
Description: R-based computational framework for a comprehensive in silico 
    analysis of circRNAs. This computational framework allows to combine and 
    analyze circRNAs previously detected by multiple publicly available 
    annotation-based circRNA detection tools. It covers different aspects of 
    circRNAs analysis from differential expression analysis, evolutionary 
    conservation, biogenesis to functional analysis.
License: GPL-3
Encoding: UTF-8
LazyData: TRUE
biocViews: Annotation, StructuralPrediction, FunctionalPrediction, GenePrediction, GenomeAssembly
Depends: 
    R(>= 3.6.0), 
    gwascat
RoxygenNote: 6.1.1
Suggests: 
    testthat,
    knitr,
    roxygen2,
    rmarkdown,
    citr,
    devtools,
    gridExtra,
    ggpubr,
    VennDiagram,
    BSgenome.Mmusculus.UCSC.mm9,
    BSgenome.Hsapiens.UCSC.hg38,
    BSgenome.Mmusculus.UCSC.mm10,
    remotes,
Imports:
    dplyr,
    magrittr,
    readr,
    rtracklayer,
    stringr,
    Biostrings,
    BSgenome,
    stringi,
    DESeq2,
    edgeR,
    GenomicRanges,
    IRanges,
    seqinr,
    R.utils,
    reshape2,
    ggplot2,
    utils,
    rlang,
    S4Vectors,
    stats,
    AnnotationHub,
    GenomeInfoDb,
    BSgenome.Hsapiens.UCSC.hg19
VignetteBuilder: 
    knitr

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

4396a9c changes package version number from 0.1.1 to 0.99.... d8d13f6 Removed files.... 82d2ffa add .Rproj and .Rproj.user/ to git ignore d454c1f Delete circRNAprofiler.Rproj 147e30b added *.Rproj to gitignore 7be826b Added comment tag # to the code in the @examples ... 12e62b6 Merge branch 'develop'

bioc-issue-bot commented 5 years ago

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: "TIMEOUT". 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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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

71aa0cb Version: 0.99.0 to Version: 0.99.1 120d4cb Added the comment tag # to avoid running the test ... 046fac2 Merge branch 'develop'

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

32109c3 Version: 0.99.1 to Version: 0.99.2 ce62d8d optimization examples 42983c3 optimization tests

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

ee170ab Version: 0.99.2 to Version: 0.99.3 8c7910e deleted test 5ca5378 update doc

bioc-issue-bot commented 5 years ago

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Liubuntu commented 5 years ago

Hi @Aufiero

Thanks for submitting your package to Bioconductor. An official review will be given shortly (within 2 weeks of last successful build).

Cheers, Qian

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

c8077d7 fix typo 5e44dc7 introduced grey scale color for plots e22653c Version: 0.99.4 to Version: 0.99.5

bioc-issue-bot commented 5 years ago

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Liubuntu commented 5 years ago

Hi @Aufiero ,

Here is part of your package review. I will post the 2nd half soon. Please seek to address the issues listed, and comment back here with updates / questions.

Best, Qian

DESCRIPTION

LazyData: field: For packages that include data, we recommend not including LazyData: TRUE. This rarely proves to be a good thing. In our experience it only slows down the loading of packages with large data.
BugReports: field: It is encouraged to include the relevant links to Github for reporting Issues.
URL: field: This field directs users to source code repositories, additional help resources, etc; It is recommended to include the link here.

R/

initCircRNAprofiler.R

L53: use file.path() instead of paste(sep="/") here, so that it could automatically adjust the separator based on different OS.
L97, use the file.path() to construct the file path instead of the paste0(). Same applies to the ther get*Tamplate functions.
This is trivial, but is it typo in the get*Tamplate() functions? Maybe you meant Template?

checkProjectFolder.R

L137, L157, L176: With your current check using %in%, an edge case maybe that the file has 2 or more columns named as id, although not very likely, but you never know and may be helpful to test. So maybe just using colnames()=="id" or adding ncol() == 1 to exclude the edge case.

getBackSplicedJunctions.R

L52: use if (nrow(experiment)) and remove the >0 and it will work sufficiently here.
L67: use file.path() here for constructing a file path.

filterCirc.R

L68: use if(nrow(experiment)) to avoid checking twice.

General

For functions that return a data.frame as output, you may consider using DataFrame instead, which basically has the same characteristics as data.frame and has a better show method. You can try using DataFrame(data.frame(letters, LETTERS)) and compare with an ordinary data.frame to have a feel.

man/

formatGTF.Rd:L10. typo, remove one the from the sentence.
getBackSplicedJunctions.Rd:L17. The list-like format can be generated by using the follow inside the .Rd file: \describe{ \item{1}{description about 1} \item{2}{... } }

vignette

Installation: you should show users how to download the package as if the package is already included in Bioconductor. E.g.,

BiocManager::install("circRNAprofiler")

You can also download the development version on github using BiocManager:

BiocManager::install("Aufiero/circRNAprofiler")

L301: Based on my understanding, should it be "extendable" instead of "extended" here?

Aufiero commented 5 years ago

Thanks Qian, I addressed all of the issues, except for the following 2.

About LazyData. If I use LazyData = FALSE, I get an error during the R CMD check when creating the vignettes. data in the package are used in the vignettes as well as in the @examples section of the functions. Shall I keep LazyData = TRUE?

-About the use of DataFrame The show method is indeed better. I did a test with the getBackSplicedJunctions() and mergeBSJunctions() functions. The output of getBackSplicedJunctions() is the input of mergeBSJunctions(). For the getBackSplicedJunctions() I returned a DataFrame object instead of a data.frame. I gave the DataFrame object to mergeBSJunctions() and I got the following error:

Error in UseMethod("mutate") : no applicable method for 'mutate' applied to an object of class "c('DataFrame', 'DataTable', 'SimpleList', 'DataTable_OR_NULL', 'List', 'Vector', 'list_OR_List', 'Annotated')"

mutate is a method of dplyr package. It seems that it does not work on a DataFrame object. Since I use a lot the dplyr package in the functions of circRNAprofiler I would prefer to keep the object data.frame also because I do not know how many issues it may cause if I change it.

S

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

f0adb65 Version: 0.99.5 to Version 0.99.6 72ce702 updated vignettes fd5737e updated Readme 2b05592 updated man doc with describe field 55a9a70 used file.path() insted of paste. corrected typo: ... bbd1dc9 typo ab13509 Added ncol() 5559f15 updated roxygem doc and fix typo 4781571 updated roxygen doc, used file.path() insted of pa...

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

214e684 fixed vignettes d95bdc5 Version: 0.99.6 to Version: 0.99.7

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

afe2880 update images color bcd5026 premoved unneeded package c38fcf8 version 0.99.7 to version 0.99.8

bioc-issue-bot commented 5 years ago

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: "TIMEOUT, 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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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

afe2880 update images color bcd5026 premoved unneeded package c38fcf8 version 0.99.7 to version 0.99.8

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

da099cd typo 3756b1a Version 0.99.10 to Version 0.99.11

bioc-issue-bot commented 5 years ago

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.

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

91310e8 test renamed file and function 50cd41c test renamed file and fucntion liftBSJcoords 8bcdc0f Version 0.99.11 to Version 0.99.12

bioc-issue-bot commented 5 years ago

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.

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

91310e8 test renamed file and function 50cd41c test renamed file and fucntion liftBSJcoords 8bcdc0f Version 0.99.11 to Version 0.99.12

bioc-issue-bot commented 5 years ago

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: "TIMEOUT". 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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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

91310e8 test renamed file and function 50cd41c test renamed file and fucntion liftBSJcoords 8bcdc0f Version 0.99.11 to Version 0.99.12

bioc-issue-bot commented 5 years ago

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: "TIMEOUT, 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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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

91310e8 test renamed file and function 50cd41c test renamed file and fucntion liftBSJcoords 8bcdc0f Version 0.99.11 to Version 0.99.12

bioc-issue-bot commented 5 years ago

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Liubuntu commented 5 years ago

Hi @Aufiero ,

Sorry for the delay of responding. I have just reviewed the rest of your package, here are the comments:

R/

getDeseqRes.R

L83, use if (nrow(experiment)) only to avoid double checking.
same for getEdgerRes.R: L87, and annotateRepeats.R: L154.
Prefix . for the non-exported, utility functions, such as getEdgerResDF and getDeseqResDF. See here for details.

unit tests

Looks good!

For your question about using DataFrame, you are fine to use the data.frame to get the best interoperability with dplyr grammars.

Bioconductor usually recommends removing the whole lazyData field from DESCRIPTION file. Your problem of R CMD CHECK doesn't seem to be related to the lazyData. But I'll try to reproduce to see if there is any other problem.

Best, Qian

Liubuntu commented 5 years ago

Hi @Aufiero ,

I couldn't reproduce your error with R CMD CHECK. Can you remove the lazyData: TRUE field from your DESCRIPTION file, and redo the check to see if the result will change?

Qian

Aufiero commented 5 years ago

Hi Qian,

-About lazyData: I removed the lazyData field from the DESCRIPTION file and I ran the R CMD check. This is the error that I get (see attached file) check.txt

-About the Prefix . for the non-exported functions: shall I rename for example getEdgerResDF to .getEdgerResDF, right? Except getEdgerResDF and getDeseqResDF there are also other non- exported functions in my package, shall I rename all of them using the prefix ''."?

Liubuntu commented 5 years ago

Hi @Aufiero ,

For your 2nd question, yes. It would be a good practice in developing R packages, by prefixing "." for non-exported functions. Highly recommended to make updates for all cases.

For the other review points, if you find similar cases, just update them all, not restricted to those I mentioned.

For the 1st question, first, you need to correct your vignette .Rmd file, L356, into eval=TRUE. Rerun the R CMD check, you should see some other errors in examples, and test functions as listed below. Fix all until you get a clean report, let me know for any questions.

errors in example and test function, in getRegexPattern.R script. the
- circRNAprofiler::inpac usage , what is it?
getMirSite.R: remove the # comment signal for the example of getMiRsite().
You should never use setwd in your scripts!!
- Instead, use following code to avoid the separator confusion on different building machine. (mac/windows/linux)
```
dir <- system.file("tests", "testthat", "testdata", package = "circRNAprofiler")
system.file(dir, "gencodeVM16.gtf")
```
- test failed in test_getMirSites.R. But also update all other functions that including setwd().

Qian

Aufiero commented 5 years ago

Hi Qian,

-I added prefix "." for non-exported functions -I removed the # comment signal for the example of getMiRsite() -R CMD check now ends with no error without the lazyData field from the DESCRIPTION file

-about setwd for my package to work the user needs to set the project folder as working directory. The project folder contains project files and the circRNA prediction results. The package circRNAprofiler assumes that the circRNA prediction results are put in specific subfolders of the project folder. The names of the files containing the circRNA prediction results are specified in a file named experiment.txt.

Since I can not use system.file to point to circRNA prediction results for the unit test I need to set testdata as working directory. Can use file.path with setwd? In this way it should be ok on different building machines. setwd(file.path(getwd(), "testdata"))

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

a219b98 Added prefix "." for non-exported functions 415019e fixed vignettes, removed eval = FALSE 917451d fixed tests 370c6fb Version: 0.99.12 to Version: 0.99.13 47311a4 fixed vignettes

bioc-issue-bot commented 5 years ago

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.

Liubuntu commented 5 years ago

Hi @Aufiero ,

Since the check is OK, and the setwd didn't trigger any building error, I'll let it pass. Thank you for the contribution to Bioconductor.

Cheers, Qian

bioc-issue-bot commented 5 years ago

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.

Thank you for contributing to Bioconductor!

mtmorgan commented 5 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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/Aufiero.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("circRNAprofiler"). The package 'landing page' will be created at

https://bioconductor.org/packages/circRNAprofiler

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

circRNAprofiler #1133

DESCRIPTION

R/

man/

vignette

R/

unit tests