[Bioc-devel] Urgent minor deployment of a release?

[Park, Adam Keebum]

Hi all,

I wonder if there is any room for deploying a modification to a released 
library(retrofit, 3.17), which was released last month.

We are in a progress of a paper review, so the release schedule (twice each 
year) does not perfectly fit our need.

Or do you think we should have used "devel" for such purposes?

Sincerely,
Adam.

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[Bioc-devel] 5mb limit for packfiles in .git is too harsh

[Park, Adam Keebum]

Dear community,

First, I want to appreciate Nathan's amazing help on my two previous inquiries. 
The answers effectively led me to pinpoint the issue.

 The final decision I made after hours of analysis was to remove all data files 
exceeding 50k sizes from the git history. However, such practice is not 
sustainable and actually is pathological because it invalidates virtually all 
previous data files and hence hampers reproducibility of previous commits, 
especially unit testing. Therefore, I want to leave a message here with a hope 
to reach administrators of bioconductor.

 I would claim that this policy should be relaxed at least for the git 
packfile. Most of us know that the .pack file residing in .git/objects/pack has 
frequently been accused by BiocChecker() for its large size (as in 
here or 
here), 
which is natural due to the purpose of packfiles: storing "all removal history" 
in a single compact 
space.
 Compressing the whole git history in a file is effective only until the 
majority of delta are sentence-based changes in a text source file for example. 
In my practice, however, a modification in blob files tended to contribute much 
more because of boosted delta after compressing datasets where some 
modification has shaken their bit patterns. Such changes were still 
kilobyte-level, but gradually impacted the whole pack file size so I had to 
remove those cases. The current policy therefore forces deletions of kilo-sized 
files in git history, not just 'large' files...
 I might not be the only one using multiple 100kb-sized experimental data in 
unit testing and vignettes. Containing dozens of such files in a 5mb package 
might be acceptable. I believe the same can hold for the pack file because it 
just represents a collection of previous files which are still less than 5mb. I 
guess the policy can relax such file size limit to allow safer and reproducible 
developer practices.

Sincerely,
Adam.


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[Bioc-devel] BFG repo cleaner did not perfectly work

[Park, Adam Keebum]

Dear community,

This is a compact version of the same issue I sent last week, for asking a 
general advice.

  *   Running the recommended command below did not perfectly remove every such 
file.

bfg --strip-blobs-bigger-than 5M repo.git

  *   The BiocChecker still picks up a pack file and emits a warning 
(.git/objects/pack-xxx..xxx.pack).

  *   However, the reference is not detected by tools like git-branch-filter or 
bfg.

I would appreciate any kinds of an advice for digging into this problem.

Sincerely,
Adam.

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[Bioc-devel] pack files not deleted from .git history

[Park, Adam Keebum]

Dear community,

I am desperately seeking a savor floundering in a pitfall for a few days. 

I have used BFG Repo-Cleaner for deleting files over 5mb in the git history. 
(Thanks to a recommendation from the community!)
However, BioChecker is still emitting warning messages pointing out a .pack 
file every time I run it.

I have used multiple different commands to delete some of them (e.g. git 
filter-branch) but none perfectly saved me. It seems endlessly many are still 
left. (While BFG says no large files remain in the repo!)

The most frustrating part is that I cannot even list them out.
For example, the official git codes below do not output any suspiciously large 
files.
​```
objects=`git verify-pack -v .git/objects/pack/pack-*.idx | grep -v chain | sort 
-k3nr `
for y in $objects
do
size=$((`echo $y | cut -f 5 -d ' '`))
sha=`echo $y | cut -f 1 -d ' '`
info=`git rev-list --all --objects | grep $sha`
output="${output}\n${size},${info}"
done
​```

Could anyone used to this issue help me?

Sincerely,
Adam.


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[Bioc-devel] Large vignettes

[Park, Adam Keebum]

Dear community,

I hope wonderful things happen to you in the new year.

I guess this issue is well-known.
BiocCheck works on a output of R CMD build, which means vignettes are rendered 
in html forms. Those sometimes include many images easily exceeding 5mb limit, 
failing the BiocCheck with a warning.

Could anyone give advice for it? I don't consider using any sort of 
pre-computed images.

Sincerely,
Adam.

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[Bioc-devel] data extension preference

[Park, Adam Keebum]

Dear whom it may concern,

I want to check if reviewers have a preference in data formats for data 
included in a package.
Is rda strongly recommended over csv?

Sincerely,
Adam.

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[Bioc-devel] bioconductor package testing

[Park, Adam Keebum]

Dear whom it may concern,

I hope I am contacting the right person for my inquiry.

(1) I wonder how I can test a package in advance of submitting to bioconductor, 
 especially with respect to dependencies. Dozens of R libraries should be 
installed with my package.

That is, I would like to simulate BiocManager::install("my package") and check 
if a fresh new user can run tutorials and vignettes code without any problem.

(2) Similarly, how could I simulate running Vignette codes in my local 
environment? As I understood so far, codes written in a Vignette(.Rmd) will be 
executable after being converted to a html document and being published in the 
bioconductor website.

Sincerely,
Adam.

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