rifiComparative

[lyoussar]

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

• Repository: https://github.com/CyanolabFreiburg/rifiComparative

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[lyoussar]

I did not get any feedback!

[lshep]

@lyoussar sorry for the delay. I will be taking over the review. I will look over the package over the next week and get back to you.

[vjcitn]

Hi @lyoussar owing to various issues I will take over the review here.

[vjcitn]

Note that when I install the latest version of rifi I see

Note: next used in wrong context: no loop is visible 
** help
Warning: apply_Ttest_delay.Rd:55: unexpected '}'
Warning: predict_ps_itss.Rd:57: unexpected '}'
*** installing help indices

[lyoussar]

The package is rifiComparative and not rifi. Could you confirm please that you are checking on the right folder?

[vjcitn]

Notice the chapter numbering in the vignette. Perhaps you need to remove a "#"

[lyoussar]

I am sorry I don t get it. What chapter do you mean? I don t see the "#" on the picture unless if its inside a chapter but I would like to know which one is. Thanks

[vjcitn]

In the vignette I see

data(stats_se_cdt1)
data(stats_se_cdt2)
data(differential_expression)
inp_s <-  
    loading_fun(stats_se_cdt1, stats_se_cdt2, differential_expression)[[1]]
head(inp_s, 5)
##   strand position ID FLT intensity probe_TI flag position_segment     delay
## 1      +       67  1   0  1367.080       -1    _              S_1 1.4190839
## 2      +      153  2   0  3316.336       -1    _              S_1 1.9343216
## 3      +      199  3   0  1112.101       -1    _              S_1 0.6442441
## 4      +      259  4   0  2012.294        1    _              S_1 0.0010000
## 5      +      320  5   0  1627.467       -1    _              S_1 1.9506707

Could the output data be represented as a GRanges, to help with interoperability and self-description. The function name loading_fun is very peculiar, too generic -- the function name should help the user understand what is being loaded. This will aid users in remembering how to use the tool.

[vjcitn]

When I render your vignette, I see the 0.x.y in the table of contents that is shown in the photograph attached to the comment. Your vignette code has

## 0. Installation

It should not have ## and should not have 0. Let the render() function take care of the numbering for you.

[vjcitn]

All the numbers in the section headings should come out (roman numerals or arabic numeral 0).

[vjcitn]

<br/><br/>
``` {r, echo = FALSE, fig.cap = "**\\label{fig:figs}Decay rate vs. Synthesis rate**", out.width = '100%'}
knitr::include_graphics("Decay_rate_vs_Synthesis_rate.png")

You are including a number of static precomputed images.  Are the computations too slow to have them performed in the vignette?  A basic purpose of the vignette discipline in Bioconductor is to illustrate the actual computations and to have the build system perform them on a regular basis, so that developers can learn if code has become stale and throws new errors.

[lyoussar]

I submitted this package on July 2022 and I made all changes the referee proposed and asked for. RifiComparative is a continuation of rifi package which was published in Bioconductor. To make the package easy and straightforward for users I submitted to Bioconductor making both packages uniforme regarding the installation and format. I followed all instructions of Biocoinductor. I made all changes the referee asked for which were a hell of work trying to keep the same format I used for the vignette in rifi. I am not sure why rifi package was accepted after slights changes in the vignette and the successor is taking a while to be accepted. I am the author of rifi and rifiComparative vignette. I am still getting request over and over even though a huge changes were applied on Aug2, Aug15, Sep1, Oct8 and Oct16.

Your last question for instance: You are including a number of static precomputed images. Are the computations too slow to have them performed in the vignette? A basic purpose of the vignette discipline in Bioconductor is to illustrate the actual computations and to have the build system perform them on a regular basis, so that developers can learn if code has become stale and throws new errors

In rifi package, I tried to put the code as the vignette discipline in Bioconductor requests but I ve got complains from the referee because the computations were slow and could be replaced by images in some cases. Now I get the opposite complain.

If you check again the rifi and rifiComparative you will find a lot of similarities although excessive changes were included on the last one because they were requested but not on the first package. I wish we can include rifiComprative in Bioconductor otherwise it will be unfortunate for the users to use rifi and not rifiComparative.

[bioc-issue-bot]

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[lshep]

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

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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("rifiComparative"). The package 'landing page' will be created at

https://bioconductor.org/packages/rifiComparative

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.