Contributions bedbaser

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Repository: https://github.com/waldronlab/bedbaser

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Aug 26 '24 14:08 jwokaty

Hi @jwokaty

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: bedbaser
Title: A BEDbase client
Version: 0.99.0
Authors@R: c(
    person(
        given = "Jen",
        family = "Wokaty",
        role = c("aut", "cre"),
        email = "[email protected]",
        comment = c(ORCID = "0009-0008-0900-8793")
    ),
    person(
        given = "Levi",
        family = "Waldron",
        role = c("aut"),
        email = "[email protected]",
        comment = c(ORCID = "0000-0003-2725-0694")
    ))
Description: A client for BEDbase. bedbaser provides access to the API at
    api.bedbase.org. It also includes convenience functions to import BED files
    into GRanges objects and BEDsets into GRangesLists.
URL: https://github.com/waldronlab/bedbaser
BugReports: https://github.com/jwokaty/bedbaser/issues
biocViews: Software, DataImport, ThirdPartyClient
License: Artistic License 2.0
Imports:
    AnVIL,
    BiocFileCache,
    dplyr,
    GenomicRanges,
    httr,
    methods,
    purrr,
    rtracklayer,
    rlang,
    R.utils,
    stats,
    stringr,
    tibble,
    tidyr,
    tools,
    utils
Suggests:
    BiocStyle,
    knitr,
    liftOver,
    testthat (>= 3.0.0)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/testthat/edition: 3

Aug 26 '24 14:08 bioc-issue-bot

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Sep 04 '24 16:09 bioc-issue-bot

Dear Package contributor,

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

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

Congratulations! The package built without errors or warnings on all platforms.

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): bedbaser_0.99.0.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 [email protected]:packages/bedbaser to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Sep 04 '24 17:09 bioc-issue-bot

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

Sep 11 '24 18:09 bioc-issue-bot

Hi @jwokaty,

I don't recommend using dependencies=TRUE when installing packages. Sticking to the default is usually preferred and is the norm. The problem with dependencies=TRUE is that it will not only include suggested packages, which would be ok if it was just doing that, but it will also include the suggested packages of the suggested packages, and so on, in a recursive manner. To be more precise, it will build the tree of dependencies by including suggested packages at all levels of the tree. This typically ends up with a tree that is much bigger than when sticking to the default. In other words, it will usually trigger download and installation of many unnecessary packages, with many of them having nothing to do with your package.

By default (i.e. when dependencies is not set or is set to NA), only the deps that are strictly required get downloaded and installed, which is what a standard installation should do.

This unit test fails for me (test-bedbaser.R, line 93):

library(testthat)
library(bedbaser)
api <- BEDbase()
id <- "b7cb28278e4cba2dc62e51ddc70cfbfb"
md <- bb_metadata(api, id, TRUE)
expect_equal("bed3+0", md$bed_type)
# Warning message:
# In readLines(file, warn = readLines.warn) :
#   incomplete final line found on '/tmp/Rtmp2hRWMP/filecbc929261744'
# Error: "bed3+0" (`actual`) not equal to md$bed_type (`expected`).
#
# `actual`:   "bed3+0"
# `expected`: "bed6+4"

See my sessionInfo() below.

Also, is there anything that can be done about the above warning? Maybe it's not harmful but it suggests that something went wrong so will confuse the end user. Note that the warning also shows up in the rendered vignette.
For people like me who are unfamiliar with the AnVIL package and its operations() accessor for Service objects, the long output of operations(api) in the vignette is quite cryptic. What is this all about? The man page for operations in the AnVIL package didn't help me either. Providing a little bit of context/explanations in your vignette would help a long way.

Using quietly=TRUE does not make the progress bar disappear:

> aa <- bb_to_granges(api, ex_bed$id, quietly=TRUE)
  |======================================================================| 100%

Maybe it should?

Also calling bb_to_granges() a second time on the same id displays the progress bar again. This suggests that the BED file is being downloaded again. Is it? Or does it get retrieved from the cache the second time? If the latter, then maybe the progress bar is not needed.

Thanks, H.

sessionInfo():

R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 23.10

Matrix products: default
BLAS:   /home/hpages/R/R-4.4.0/lib/libRblas.so 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome.Hsapiens.UCSC.hg38_1.4.5
 [3] BSgenome_1.73.1                   rtracklayer_1.65.0               
 [5] BiocIO_1.15.2                     Biostrings_2.73.2                
 [7] XVector_0.45.0                    GenomicRanges_1.57.1             
 [9] GenomeInfoDb_1.41.1               IRanges_2.39.2                   
[11] S4Vectors_0.43.2                  BiocGenerics_0.51.2              
[13] bedbaser_0.99.0                   testthat_3.2.1.1                 

loaded via a namespace (and not attached):
 [1] DBI_1.2.3                   bitops_1.0-8               
 [3] httr2_1.0.5                 formatR_1.14               
 [5] AnVILBase_0.99.27           rematch2_2.1.2             
 [7] rlang_1.1.4                 magrittr_2.0.3             
 [9] matrixStats_1.4.1           compiler_4.4.0             
[11] RSQLite_2.3.7               vctrs_0.6.5                
[13] stringr_1.5.1               pkgconfig_2.0.3            
[15] crayon_1.5.3                fastmap_1.2.0              
[17] dbplyr_2.5.0                utf8_1.2.4                 
[19] Rsamtools_2.21.2            promises_1.3.0             
[21] UCSC.utils_1.1.0            purrr_1.0.2                
[23] bit_4.5.0                   waldo_0.5.3                
[25] zlibbioc_1.51.1             cachem_1.1.0               
[27] jsonlite_1.8.9              blob_1.2.4                 
[29] later_1.3.2                 DelayedArray_0.31.12       
[31] BiocParallel_1.39.0         parallel_4.4.0             
[33] R6_2.5.1                    stringi_1.8.4              
[35] brio_1.1.5                  Rcpp_1.0.13                
[37] SummarizedExperiment_1.35.2 R.utils_2.12.3             
[39] BiocBaseUtils_1.7.3         httpuv_1.6.15              
[41] Matrix_1.7-0                tidyselect_1.2.1           
[43] rstudioapi_0.16.0           abind_1.4-8                
[45] yaml_2.3.10                 codetools_0.2-20           
[47] miniUI_0.1.1.1              curl_5.2.3                 
[49] lattice_0.22-6              tibble_3.2.1               
[51] shiny_1.9.1                 Biobase_2.65.1             
[53] withr_3.0.1                 desc_1.4.3                 
[55] lambda.r_1.2.4              futile.logger_1.4.3        
[57] BiocFileCache_2.13.0        pillar_1.9.0               
[59] BiocManager_1.30.25         filelock_1.0.3             
[61] MatrixGenerics_1.17.0       DT_0.33                    
[63] generics_0.1.3              AnVIL_1.17.15              
[65] RCurl_1.98-1.16             xtable_1.8-4               
[67] glue_1.8.0                  tools_4.4.0                
[69] diffobj_0.3.5               GenomicAlignments_1.41.0   
[71] rapiclient_0.1.8            XML_3.99-0.17              
[73] grid_4.4.0                  tidyr_1.3.1                
[75] GenomeInfoDbData_1.2.13     restfulr_0.0.15            
[77] cli_3.6.3                   rappdirs_0.3.3             
[79] futile.options_1.0.1        fansi_1.0.6                
[81] S4Arrays_1.5.10             dplyr_1.1.4                
[83] R.methodsS3_1.8.2           digest_0.6.37              
[85] SparseArray_1.5.41          rjson_0.2.23               
[87] htmlwidgets_1.6.4           memoise_2.0.1              
[89] htmltools_0.5.8.1           R.oo_1.26.0                
[91] lifecycle_1.0.4             httr_1.4.7                 
[93] mime_0.12                   bit64_4.5.2

Oct 01 '24 19:10 hpages

Received a valid push on git.bioconductor.org; starting a build for commit id: 76f4919a9c0b40d56ccab36c83916374555c952a

Oct 08 '24 00:10 bioc-issue-bot

Dear Package contributor,

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

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

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): bedbaser_0.99.1.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 [email protected]:packages/bedbaser to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 08 '24 00:10 bioc-issue-bot

@hpages Thanks for the thoughtful review. I tried to address all points in the code.

I removed dependences = TRUE.
The bedbase team reuploaded files and that particular file changed from one bed type to another, which is why it failed. I reached out to them about it and selected another bed file that should pass the test.
I have filed a ticket with the bedbase team to ask if they could add an extra line to api file to prevent the warning from happening. I have also suppressed the warning in bedbaser.
I moved and rewrote the section about the AnVIL Service class and used show rather than operations, which I hope will make the intention clearer about how it can be used.
I could not find a way to silence the progress bar, which is coming from BiocFileCache, but I also think bedbaser shouldn't silently download things.
Yes, it was downloading twice. I thought the example I mostly copied from BiocFileCache would check if the resource should be updated then download, but it was always downloading because the last modified date and etags never seem to get set. I removed the part that would download again.

Oct 08 '24 00:10 jwokaty

Received a valid push on git.bioconductor.org; starting a build for commit id: 60a64166a13ae9d1f5f9bc2a64f1fd5d39ca634f

Oct 09 '24 14:10 bioc-issue-bot

Dear Package contributor,

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

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

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): bedbaser_0.99.2.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 [email protected]:packages/bedbaser to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 09 '24 14:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 5b633084e803a5104f5606aa91d416ebd1e625b4

Oct 10 '24 03:10 bioc-issue-bot

Dear Package contributor,

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

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

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): bedbaser_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 [email protected]:packages/bedbaser to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 10 '24 03:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 58f6b285f975bf6fa0fb935fe1d0b7d0603e1045

Oct 16 '24 14:10 bioc-issue-bot

Dear Package contributor,

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

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

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): bedbaser_0.99.8.tar.gz

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/bedbaser to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 16 '24 14:10 bioc-issue-bot

Thanks Jen for the changes.

I could not find a way to silence the progress bar, which is coming from BiocFileCache,

I see that BiocFileCache::bfcadd() uses GET(url, progress(con=stderr())) under the hood to download the file: https://github.com/Bioconductor/BiocFileCache/blob/7c5d63e9728b4bf159c988dc627bd16a0c2b6f71/R/httr.R#L64-L65

Unfortunately, there doesn't seem to be an easy way to silence this, indeed. Bummer!

but I also think bedbaser shouldn't silently download things.

Well, that's what bb_save() does, doesn't it?

bb_save(api, ex$id, tempdir())  # silent download

Unless quietly is set to FALSE:

bb_save(api, ex$id, tempdir(), quietly=FALSE)

# trying URL 'https://data2.bedbase.org/files/0/4/04c46b96264ef40bca93f03b10345da5.bed.gz'
# Content type 'binary/octet-stream' length 67639 bytes (66 KB)
# ==================================================
# downloaded 66 KB

A few more things:

I'm surprised by the fact that bb_list_beds() lists extactly 1000 files! Is this really the number of BED files available on BEDbase or is the full list truncated somehow? Also querying the BEDbase REST API directly with httr reports different numbers of BED files and BEDsets currently available:
```
library(httr)
res <- GET("https://api.bedbase.org/v1/stats")
content(res, "text", encoding="UTF-8")
# [1] "{\"bedfiles_number\":8917,\"bedsets_number\":171,\"genomes_number\":19}"
```

There are 2 BiocCheck warnings on the latest SPB report that are worth your attention (items 8 and 9 below). Unfortunately, for some reason the SPB didn't catch them.

First BiocCheck warning:
```
✔ Checking coding practice... [4ms]
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• utils.R (line 53, column 30)
```
The fix is simple: use is(cache_or_path, "BiocFileCache") instead of class(cache_or_path) == "BiocFileCache". The first one is preferred because it will also return TRUE on an object that belongs to a subclass of BiocFileCache. Even if the BiocFileCache class has no children at the moment (AFAIK), someone could define such a subclass, say MyBiocFileCacheExtension. For example:
```
setClass("MyBiocFileCacheExtension", contains="BiocFileCache")

## Constructor:
MyBiocFileCacheExtension <- function(...) new("MyBiocFileCacheExtension", BiocFileCache(...))

bfc_ext <- MyBiocFileCacheExtension()

bfc_ext
# class: MyBiocFileCacheExtension
# bfccache: /home/hpages/.cache/R/BiocFileCache
# bfccount: 60
# For more information see: bfcinfo() or bfcquery()

class(bfc_ext)
# [1] "MyBiocFileCacheExtension"
# attr(,"package")
# [1] ".GlobalEnv"
```
If you use if (class(cache_or_path) == "BiocFileCache"), your code will fail to detect that cache_or_path is actually a BiocFileCache object (or derivative), and so it will branch to the else part of the if statement where bad things will happen. But if you use is(bfc_ext, "BiocFileCache"), everything will be fine:
```
is(bfc_ext, "BiocFileCache")
# [1] TRUE
```
Second BiocCheck warning:
```
✔ Checking man page documentation... [3ms]
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/bb_save.Rd
```
All functions in R return something even if they don't seem to. When a function doesn't seem to return anything that's because it returns something invisible, like an invisible NULL. This is actually the case for your bb_save() function. Like many other "save" functions in R/Bioconductor, it returns an invisible NULL:
```
api <- BEDbase()
ex <- bb_example(api, "bed")
res <- bb_save(api, ex$id, tempdir())
res
# NULL
```
In this case, the Value section in the man page just needs to say something like "An invisible NULL." See for example the man pages for saveRDS() in packages base and BiocGenerics.
How about wrapping occurences of bedbaser in `r Biocpkg(...)` like you did for other package names in the vignette? This will generate links that are temporarily invalid but they will become valid once the package has a landing page.

Thanks, H.

@lshep @LiNk-NY Looks like BiocCheck warnings are not seen by the SPB (see latest report for bedbaser above).

Oct 21 '24 00:10 hpages

Received a valid push on git.bioconductor.org; starting a build for commit id: 29683e6896beecd353721107258d0fdf38c1e0a6

Nov 13 '24 20:11 bioc-issue-bot

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: "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.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): bedbaser_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 [email protected]:packages/bedbaser to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Nov 13 '24 20:11 bioc-issue-bot

@jwokaty Let me know when it's time for me to take another look. Thanks!

Nov 21 '24 21:11 hpages

Received a valid push on git.bioconductor.org; starting a build for commit id: 371c3881cea86293a7e2384493acbeedbf9eb552

Dec 03 '24 07:12 bioc-issue-bot

Dear Package contributor,

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

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

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Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): bedbaser_0.99.11.tar.gz

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/bedbaser to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Dec 03 '24 07:12 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 8ed4b2ed38c54bb265c03119e86a5bc1581506ee

Dec 03 '24 17:12 bioc-issue-bot

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: "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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The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): bedbaser_0.99.12.tar.gz

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Dec 03 '24 17:12 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 59fe2e1b9e0e63a8fbd6a3cc9ad46f4ffee879c5

Jan 03 '25 16:01 bioc-issue-bot

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.

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The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): bedbaser_0.99.15.tar.gz

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Jan 03 '25 16:01 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 6ab027bb671884016a79ddc3b14832bb33762705

Jan 03 '25 18:01 bioc-issue-bot

Dear Package contributor,

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

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

Congratulations! The package built without errors or warnings on all platforms.

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The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): bedbaser_0.99.16.tar.gz

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Jan 03 '25 18:01 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 115745a5541b7fb904fc4ccdfd5d1532f307f8c4

Jan 03 '25 23:01 bioc-issue-bot

Dear Package contributor,

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

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

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): bedbaser_0.99.17.tar.gz

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Jan 03 '25 23:01 bioc-issue-bot

@jwokaty Is it time for me to take another look?

Jan 08 '25 00:01 hpages

Received a valid push on git.bioconductor.org; starting a build for commit id: 2bf6e04ec9c252b66ed0e3ad53c3cb7b491ca0d2

Jan 15 '25 17:01 bioc-issue-bot