add support for Bioconductor #58 #59

schochastics · 2023-02-19T07:27:50Z

@chainsawriot Draft so you can monitor the progress

codecov-commenter · 2023-02-19T07:53:01Z

Codecov Report

Merging #59 (b723ed6) into v0.2 (a9bb935) will decrease coverage by 0.21%.
The diff coverage is 92.23%.

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@@            Coverage Diff             @@
##             v0.2      #59      +/-   ##
==========================================
- Coverage   93.64%   93.44%   -0.21%     
==========================================
  Files           5        5              
  Lines         535      625      +90     
==========================================
+ Hits          501      584      +83     
- Misses         34       41       +7

Impacted Files	Coverage Δ
R/as_pkgrefs.R	`90.90% <50.00%> (ø)`
R/resolve.R	`90.37% <88.00%> (-0.16%)`	⬇️
R/installation.R	`96.19% <95.65%> (-0.18%)`	⬇️
R/memo_misc.R	`100.00% <100.00%> (ø)`
R/pkgref.R	`95.00% <100.00%> (+0.88%)`	⬆️

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

schochastics · 2023-02-19T10:36:04Z

R/pkgref.R

@@ -58,6 +58,11 @@
    grepl("/", pkg)
 }

+.is_bioc <- function(pkg,bioc_version){


@chainsawriot This function requires the bioc version to check if the package is in a specific release. Couldnt find any other way to check this thus far, but this would require to also add bioc_version as a parameter to .normalize_pkg

Suggestion for .normalize_pkg(): make bioc_version optional. If it is omitted, it is assumed to be a cran package. if present, check

.normalize_pkg <- function(pkg,bioc_version = NULL) { if (pkg == "" || is.na(pkg)) { stop("Invalid `pkg`.", call. = FALSE) } if (isTRUE(.is_github(pkg))) { if (isTRUE(grepl("github\\.com", pkg))) { pkg <- .extract_github_handle(pkg) } } if (isTRUE(.is_pkgref(pkg))) { return(.clean_suffixes(pkg)) } if (isTRUE(.is_github(pkg))) { return(paste0("github::", .clean_suffixes(pkg))) } if(is.null(bioc_version)){ return(paste0("cran::", .clean_suffixes(pkg))) } else{ if(isTRUE(.is_bioc(pkg,bioc_version))){ return(paste0("bioc::", .clean_suffixes(pkg))) } else{ return(paste0("cran::", .clean_suffixes(pkg))) } } }

schochastics · 2023-02-19T19:05:34Z

R/resolve.R

@@ -12,7 +12,7 @@
  if (snapshot_date < attr(cached_biocver, "newest_date")) {
    allvers <- cached_biocver
  } else {
-    # allvers <- .memo_rver() #TODO
+    return(data.frame(version="3.16",date = "2022-11-02",rver = 4.2)) # TODO realtime check


this obviously needs to be changed eventually

schochastics · 2023-02-19T19:07:01Z

R/resolve.R

@@ -466,6 +471,13 @@ query_sysreqs <- function(rang, os = "ubuntu-20.04") {
    unique(unlist(res))
 }

+.query_sysreqs_bioc <- function(handle, os) {
+  # TODO 


checked all System Requirements on current release of Bioconductor and non of them have apt-get style. Very verbose content in general and not something we can every resolve. Current reease has like 200 pkgs with Sysreqs and most of them say "C++"

If that's vanilla C++ (probably just Rcpp or the C interface), it doesn't require any apt-get. These are all of them.

These are in the current release of bioc. So what I basically have to do is clean this output, and match it with the ones in the link you shared and add a apt install -y in front if found?

pkgs <- rang:::.memo_search_bioc("release") tst <- pkgs$SystemRequirements tst <- tst[!is.na(tst)] unique(tst) #> [1] "pandoc (>= 1.19.2.1)" #> [2] "C++11" #> [3] "gsl" #> [4] "python, pytorch, numpy" #> [5] "GNU make" #> [6] "bcl2Fastq (versions >= 2.1.7)" #> [7] "pandoc (http://pandoc.org/installing.html) for\ngenerating reports from markdown files." #> [8] "JAGS (4.3.0)" #> [9] "kallisto" #> [10] "docker" #> [11] "mailsend-go" #> [12] "python (>= 2.7), sklearn, numpy, pandas, h5py" #> [13] "Tktable, BWidget" #> [14] "Cytoscape (>= 3.6.1) (if used for visualization of\nresults, heavily suggested)" #> [15] "Graphviz version >= 2.2" #> [16] "libcurl4-openssl-dev, libxml2-dev, libssl-dev,\ngfortran, build-essential, libz-dev, zlib1g-dev" #> [17] "OpenBabel (>= 3.0.0) with headers\n(http://openbabel.org). Eigen3 with headers." #> [18] "bowtie, samtools, and egrep are required for some\nfunctionalities" #> [19] "Rtools (>= 3.1)" #> [20] "Java version >= 1.7, Pandoc" #> [21] "BUSCO (>= 5.1.3) <https://busco.ezlab.org/>" #> [22] "Perl" #> [23] "libxml2: libxml2-dev (deb), libxml2-devel (rpm)\nlibcurl: libcurl4-openssl-dev (deb), libcurl-devel (rpm)\nopenssl: libssl-dev (deb), openssl-devel (rpm), libssl_dev\n(csw), [email protected] (brew)" #> [24] "C++11, GNU make" #> [25] "GNU make, C++11" #> [26] "xml2, GNU make, C++11" #> [27] "Java (>= 1.8)" #> [28] "C++14" #> [29] "To generate html reports pandoc\n(http://pandoc.org/installing.html) is required." #> [30] "GNU make, meme, fimo" #> [31] "Ensembl VEP (API version 105) and the Perl modules\nDBI and DBD::mysql must be installed. See the package README\nand Ensembl installation instructions:\nhttp://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer" #> [32] "C++17, GNU make" #> [33] "Java (>= 8)" #> [34] "ImageMagick" #> [35] "gsl. Note: users should have GSL installed. Windows\nusers: 'consult the README file available in the inst directory\nof the source distribution for necessary configuration\ninstructions'." #> [36] "1. C++11, 2. a graphic driver or a CPU SDK. 3. ICD\nloader For Windows user, an ICD loader is required at\nC:/windows/system32/OpenCL.dll (Usually it is installed by the\ngraphic driver). For Linux user (Except mac):\nocl-icd-opencl-dev package is required. For Mac user, no action\nis needed for the system has installed the dependency. 4. GNU\nmake" #> [37] "JRE 8+" #> [38] "gtkmm-2.4, GNU make" #> [39] "JAGS 4.0.0" #> [40] "BLAT, UCSC hg18 in 2bit format for BLAT" #> [41] "4GB of RAM" #> [42] "graphviz" #> [43] "GSL and OpenMP" #> [44] "Python (>= 3.5.0), hic-straw" #> [45] "JAGS 4.x.y" #> [46] "Cytoscape (>= 3.3.0), Java (>= 8)" #> [47] "clustalo, gs, perl" #> [48] "megadepth\n(<https://github.com/ChristopherWilks/megadepth>)" #> [49] "Meme Suite (v5.3.3 or above)\n<http://meme-suite.org/doc/download.html>" #> [50] "Cytoscape (>= 3.9.0) for the cytoPath() examples" #> [51] "HMMER3" #> [52] "GNU make, PhISCS (optional)" #> [53] "Ensembl VEP, Samtools" #> [54] "glpk (>= 4.57)" #> [55] "Python (>=3), numpy, pandas, h5py, scipy, argparse,\nsklearn, mofapy2" #> [56] "mono-runtime 4.x or higher (including System.Data\nlibrary) on Linux/macOS, .Net Framework (>= 4.5.1) on Microsoft\nWindows." #> [57] "python" #> [58] "bedtools (>= 2.28.0), Stereogene (>= v2.22), CapR\n(>= 1.1.1)" #> [59] "GNU make, Bash, Perl, Gzip" #> [60] "libxml2, libSBML (>= 5.5)" #> [61] "MAFFT (>= 7.305), OligoArrayAux (>= 3.8), ViennaRNA\n(>= 2.4.1), MELTING (>= 5.1.1), Pandoc (>= 1.12.3)" #> [62] "C++ software package Random Jungle" #> [63] "Java (>= 1.6)" #> [64] "Rcpp" #> [65] "C++11, Rtools (>= 3.1)" #> [66] "C++11, GNU make, samtools" #> [67] "pandoc (>= 1.12.3)" #> [68] "nodejs" #> [69] "Cytoscape (>= 3.7.1), CyREST (>= 3.8.0)" #> [70] "None" #> [71] "Java Runtime Environment (Java>= 11)" #> [72] "hiredis" #> [73] "Java version >= 1.6" #> [74] "pyGenomeTracks (prefered to use\ninstall_pyGenomeTracks())" #> [75] "jQuery, jQueryUI, qTip2, D3js and Raphael are\nrequired Javascript libraries made available via the online\nCDNJS service (http://cdnjs.cloudflare.com)." #> [76] "optionally Graphviz (>= 2.16)" #> [77] "libbz2 & liblzma & libcurl (with header files), GNU\nmake" #> [78] "Internal files Xba.CQV, Xba.regions (or other\nregions file)" #> [79] "OpenBabel" #> [80] "Java" #> [81] ".NET 5.0" #> [82] "RNASeqR only support Linux and macOS. Window is not\nsupported. Python2 is highly recommended. If your machine is\nPython3, make sure '2to3' command is available." #> [83] "libsbml (==5.10.2)" #> [84] "python (< 3.7), tensorflow" #> [85] "Python (>= 3.6), leidenalg (>= 0.8.2)" #> [86] "c++11" #> [87] "Java (>= 1.5)" #> [88] "Python (>= 3.5), scikit-learn (>= 0.21.2),\npackaging" #> [89] "samtools" #> [90] "C++17" #> [91] "systemPipeR can be used to run external\ncommand-line software (e.g. short read aligners), but the\ncorresponding tool needs to be installed on a system." #> [92] "Primer3 (>= 2.5.0), BLAST+ (>=2.6.0)" #> [93] "Java Runtime Environment (>= 6)" #> [94] "Cytoscape >= 3.9.1" #> [95] "C++11 Windows: Dokan Linux&Mac: fuse, pkg-config" #> [96] "git" #> [97] "Unix, Perl (>= 5.6.0), Netpbm"

^{Created on 2023-02-19 with reprex v2.0.2}

schochastics · 2023-02-20T15:23:03Z

@chainsawriot should be ready now

chainsawriot · 2023-02-20T16:46:48Z

There is no caching yet. But I am checking whether caching is needed for Bioc packages in our Woody-based Docker image by manually modifying Dockerfile / rang.R.

x <- resolve("bioc::BiocGenerics", snapshot_date = "2013-08-28")
dockerize(x, "irgendwo") ## ask you to cache
dockerize(x, "irgendwo", cache = TRUE) ## no cache

Update: resolve with "bioc::BiocGenerics" likes the above wont write bioc_version to the rang object. And then export_rang won't work.

schochastics · 2023-02-20T17:24:47Z

Ah I see, I overlooked the caching part. Working on it
For resolve, you need to set query_bio in resolve() to true. Then it adds the bioc_version. Bioconductor is only queried when the user sets the parameter to true. I thought thats sensible, given that there is quite some machinery behind the bioc part that doesnt need to run unnecessarily

chainsawriot · 2023-02-20T18:18:10Z

~~bioc_mirror in https also needs to be normalize to http for R < 3.3 (R prior 3.3 doesn't support https authentication)~~

[see below]

https://github.com/chainsawriot/rang/blob/a4d93369f9ec80b555828888ea3bcec28703241a/R/installation.R#L302-L304

chainsawriot · 2023-02-20T18:20:27Z

Ah I see, I overlooked the caching part. Working on it For resolve, you need to set query_bio in resolve() to true. Then it adds the bioc_version. Bioconductor is only queried when the user sets the parameter to true. I thought thats sensible, given that there is quite some machinery behind the bioc part that doesnt need to run unnecessarily

I agree. But for explicit cases like: pkgs = bioc::BiocGenerics, should the default query_bioc = FALSE be overridden?

schochastics · 2023-02-20T18:23:07Z

yep hd the same though. I put that in the next commit

chainsawriot · 2023-02-20T18:24:00Z

I think we must enforce dockerize(cache = TRUE) even for R < 3.3 with Bioconductor packages. Bioconductor the webserver doesn't support http download. (To be exact, bioconductor will automatically convert it to https. And Debian Woody can't handle that.)
On a modern machine, it redirected to https://mghp.osn.xsede.org.

wget http://bioconductor.org/packages/2.12/bioc/src/contrib/BiocGenerics_0.6.0.tar.gz


--2023-02-20 19:25:23--  http://bioconductor.org/packages/2.12/bioc/src/contrib/BiocGenerics_0.6.0.tar.gz
Resolving bioconductor.org (bioconductor.org)... 18.66.147.62, 18.66.147.42, 18.66.147.31, ...
Connecting to bioconductor.org (bioconductor.org)|18.66.147.62|:80... connected.
HTTP request sent, awaiting response... 302 Moved Temporarily
Location: https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/2.12/bioc/src/contrib/BiocGenerics_0.6.0.tar.gz [following]
--2023-02-20 19:25:23--  https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/2.12/bioc/src/contrib/BiocGenerics_0.6.0.tar.gz
Resolving mghp.osn.xsede.org (mghp.osn.xsede.org)... 192.69.103.248, 192.69.103.246, 192.69.103.247
Connecting to mghp.osn.xsede.org (mghp.osn.xsede.org)|192.69.103.248|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 26482 (26K) [application/octet-stream]
Saving to: ‘BiocGenerics_0.6.0.tar.gz’

BiocGenerics_0.6.0.tar.gz     100%[===============================================>]  25.86K  --.-KB/s    in 0.1s    

2023-02-20 19:25:25 (222 KB/s) - ‘BiocGenerics_0.6.0.tar.gz’ saved [26482/26482]

schochastics · 2023-02-20T19:38:02Z

@chainsawriot ok I think it is done again, except maybe 2 points:

The test coverage error: Not sure I can add any meaningful test to get rid of it. Can do some low effort one to cover more lines

Should I simply change the r version reqired for caching or do another ifelse with bioc?

chainsawriot · 2023-02-20T21:45:15Z

@schochastics You may leave the testing to me.

For the cache testing

https://github.com/schochastics/rang/blob/1a04a3b4fcb6384c4ff63dffb8b0d7d81e8cdf4b/R/installation.R#L395-L399

need_cache <- (isTRUE(any(grepl("^github::", .extract_pkgrefs(rang)))) &&
               utils::compareVersion(rang$r_version, "3.1") == -1) ||
      (isTRUE(any(grepl("^bioc::", .extract_pkgrefs(rang)))) &&
       utils::compareVersion(rang$r_version, "3.3") == -1)
if (isTRUE(need_cache) && isFALSE(cache)) {
    stop("Non-CRAN packages must be cached for this R version: ", rang$r_version, ". Please set `cache` = TRUE.", call. = FALSE)
}

In the review, I indicated that the header.R isn't correct. This is how I modify it to make docker run.

.install_packages <- function(tarball_path, lib, verbose, current_r_version) {
    if (utils::compareVersion(current_r_version, "3.0") != -1) {
        if (is.na(lib)) {
            install.packages(pkg = tarball_path, repos = NULL, verbose = verbose, quiet = !verbose)
        } else {
            install.packages(pkg = tarball_path, lib = lib, repos = NULL, verbose = verbose, quiet = !verbose)
        }
    } else {
        if (is.na(lib)) {
            install.packages(pkg = tarball_path, repos = NULL)
        } else {
            install.packages(pkg = tarball_path, lib = lib, repos = NULL)
        }
    }
}

.download_package <- function(tarball_path, x, version, handle, source, uid, verbose, cran_mirror, bioc_mirror) {
    if (source == "github") {
        return(.download_package_from_github(tarball_path, x, version, handle, source, uid))
    }
    if (source == "bioc") {
          url <- paste(bioc_mirror, "bioc/src/contrib/", x, "_", version, ".tar.gz", sep = "")
    }
    if (source == "cran") {
          url <- paste(cran_mirror, "src/contrib/Archive/", x, "/", x, "_", version, ".tar.gz", sep = "")  
    }
        
    tryCatch({
        suppressWarnings(download.file(url, destfile = tarball_path, quiet = !verbose))
    }, error = function(e) {
        ## is the current latest
        url <- paste(cran_mirror, "src/contrib/", x, "_", version, ".tar.gz", sep = "")
        download.file(url, destfile = tarball_path, quiet = !verbose)
    })
    invisible(tarball_path)
}

.tempfile <- function(tmpdir = tempdir(), fileext = ".tar.gz") {
    file.path(tmpdir,
    paste(paste(sample(c(LETTERS, letters), 20, replace = TRUE), collapse = "")),
    fileext)
}

.build_raw_tarball <- function(raw_tarball_path, x, version, tarball_path) {
    tmp_dir <- .tempfile(fileext = "")
    dir.create(tmp_dir)
    system(command = paste("tar", "-zxf ", raw_tarball_path, "-C", tmp_dir))
    pkg_dir <- list.files(path = tmp_dir, full.names = TRUE)[1]
    new_pkg_dir <- file.path(tmp_dir, x)
    file.rename(pkg_dir, new_pkg_dir)
    res <- system(command = paste("R", "CMD", "build", new_pkg_dir))
    expected_tarball_path <- paste(x, "_", version, ".tar.gz", sep = "")
    stopifnot(file.exists(expected_tarball_path))
    file.rename(expected_tarball_path, tarball_path)
    return(tarball_path)
}

.install_from_source <- function(x, version, handle, source, uid, lib,
                                 path = tempdir(), verbose, cran_mirror, bioc_mirror, current_r_version) {
    tarball_path <- file.path(path, paste(x, "_", version, ".tar.gz", sep = ""))
    raw_tarball_path <- file.path(path, paste("raw_", x, "_", version, ".tar.gz", sep = ""))
    if (!file.exists(tarball_path) && !file.exists(raw_tarball_path)) {
        .download_package(tarball_path = tarball_path, x = x, version = version, handle = handle, source = source,
                          uid = uid, verbose = verbose, cran_mirror = cran_mirror, bioc_mirror = bioc_mirror)
    }
    if (file.exists(raw_tarball_path)) {
        tarball_path <- .build_raw_tarball(raw_tarball_path, x = x, version = version, tarball_path)
        if (!file.exists(tarball_path)) {
            stop("building failed.")
        }
    }
    .install_packages(tarball_path, lib, verbose, current_r_version)
    ## check and error
    if (!is.na(lib)) {
        installed_packages <- installed.packages(lib.loc = lib)
    } else {
        installed_packages <- installed.packages()
    }
    if (!x %in% dimnames(installed_packages)[[1]]) {
        stop("Fail to install ", x, "\n")
    }
    invisible()
}

# installing github packages
.download_github_safe <- function(handle, sha, file) {
    tryCatch(
        download.file(paste("http://api.github.com/repos/", handle, "/tarball/", sha, sep = ""), destfile = file),
        error = function(e) {
            stop(paste("couldn't download ", handle, " from github", sep = ""), call. = FALSE)
        }
    )
}

.tempfile <- function(tmpdir = tempdir(), fileext = ".tar.gz") {
    file.path(tmpdir,
    paste(paste(sample(c(LETTERS, letters), 20, replace = TRUE), collapse = ""), fileext, sep = ""))
}

.download_package_from_github <- function(tarball_path, x, version, handle, source, uid) {
    sha <- uid
    short_sha <- substr(sha, 1, 7)
    dest_tar <- .tempfile(fileext = ".tar.gz")
    tmp_dir <- tempdir()
    tryCatch(
        download.file(paste("https://api.github.com/repos/", handle, "/tarball/", sha, sep = ""), destfile = dest_tar),
        error = function(e) {
            .download_github_safe(handle, sha, dest_tar)
        }
    )  
    system(command = paste("tar", "-zxf ", dest_tar, "-C", tmp_dir))
    dlist <- list.dirs(path = tmp_dir, recursive = FALSE) ## TODO list.dirs is 2.14
    pkg_dir <- dlist[grepl(short_sha, dlist)] ## TODO grepl is 2.9.0
    if(length(pkg_dir) != 1) {
        stop(paste("couldn't uniquely locate the unzipped package source in ",tmp_dir, sep = ""))
    }
    res <- system(command = paste("R", "CMD", "build", pkg_dir), intern = TRUE)
    expected_tarball_path <- paste(x, "_", version, ".tar.gz", sep = "")
    if (!file.exists(expected_tarball_path)) {
        stop("Cannot locate the built tarball.")
    }
    file.rename(from = expected_tarball_path, to = tarball_path)
    return(tarball_path)
}

footer.R

## In Unix, all things are file.
## Before you complain, R <= 3.2.0 doesn't have dir.exists.
if (file.exists("cache")) {
    path <- "cache"
} else {
    path <- tempdir()
}

if (nrow(installation_order) >= 1) {
    for (i in seq(from = 1, to = nrow(installation_order), by = 1)) {
        x <- installation_order$x[i]
        source <- installation_order$source[i]
        version <- installation_order$version[i]
        handle <- installation_order$handle[i]
        uid <- installation_order$uid[i]
        .install_from_source(x = x, version = version, handle = handle, source = source, uid = uid,
                             lib = lib, path = path, verbose = verbose,
                             cran_mirror = cran_mirror, bioc_mirror = bioc_mirror,
                             current_r_version = current_r_version) 
    }
}

chainsawriot · 2023-02-20T21:51:02Z

BTW, I suggest writing bioc_mirror anyway to rang.R, NULL if there are no bioc packages.

schochastics · 2023-02-20T22:26:56Z

ok hope all suggestions are in. Sorry for the header/footer miss. Edit: well guess I broke something

schochastics · 2023-02-21T07:06:20Z

Ok the as_pkgrefs implementation is still missing for bioc

schochastics · 2023-02-21T07:56:16Z

third time's the charm: I hope everything is done now

aaah forgot this: #58 (comment)
Atm the current release is hardcoded. Suggestions?
I could contact rhub if they are interested in hosting something but that will not be done within a short time frame.

Nice, found this

schochastics · 2023-02-21T09:21:02Z

fourth time's...
tests missing but that what you wanted to do @chainsawriot ?

chainsawriot · 2023-02-21T09:56:32Z

@schochastics Yes, I will do the testing.

schochastics added 7 commits February 18, 2023 15:56

added bioc versions

1c6331b

fixed ordering error in cahced_biocver

8c34a79

added query_biocver

bd37ca5

added bioc_package_history

0907a90

cached_biocver to data.frame

160d381

fixed missing supported_os

397c891

added biocver generation

80215bb

check if pkg is bioc

7f49b93

schochastics commented Feb 19, 2023

View reviewed changes

schochastics added 4 commits February 19, 2023 12:40

fix indention

2c4da10

added is.bioc and adjusted normalize_pkg

dce1271

added query_snapshot_dependencies_bioc

db5b2f2

finalized resolve

bceff5a

schochastics commented Feb 19, 2023

View reviewed changes

schochastics added 11 commits February 19, 2023 20:14

Merge remote-tracking branch 'upstream/v0.2' into bioc

2a4feb9

added bioc support for export_rang

bcab080

probably fixed sysreqs for bioc

06564a1

fixed sysreq return value

93ece47

fixed typo

9f3cd88

added resolve test for bioc

bbdde48

added test for bioc version

37defb3

missed the dot

957fc7d

added test for new bioc release

9709762

test dockerize with bioc

5a2c69d

better bioc test data

04c70ad

schochastics marked this pull request as ready for review February 20, 2023 15:20

schochastics added 3 commits February 20, 2023 20:01

added package caching for bioc

e5997a2

set query_bioc TRUE if bioc detected

29e3b7f

added cache test for bioc

1a04a3b

cache testing,fixed header/footer, always write bioc version

0c5d1d1

integrated bioc into as_pkgref

15ab0a0

get bioc versions from online

b723ed6

chainsawriot merged commit beb9d67 into gesistsa:v0.2 Feb 21, 2023

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add support for Bioconductor #58 #59

add support for Bioconductor #58 #59

schochastics commented Feb 19, 2023

codecov-commenter commented Feb 19, 2023 •

edited

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schochastics Feb 19, 2023

schochastics Feb 19, 2023 •

edited

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schochastics Feb 19, 2023

schochastics Feb 19, 2023

chainsawriot Feb 19, 2023

schochastics Feb 19, 2023

schochastics commented Feb 20, 2023

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chainsawriot commented Feb 21, 2023

add support for Bioconductor #58 #59

add support for Bioconductor #58 #59

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