Vince Carey vjcitn
vjcitn
/ doGaussianIntegral.Rmd
Created
May 12, 2026 16:50
some tasks in integration carried out with local LLM
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| > library(ellmer) | |
| 1/4 packages newly attached/loaded, see sessionInfo() for details. | |
| > ch = chat_ollama(model="qwen3-coder:30b") | |
| > ch$chat("Discuss how to evaluate the integral of the Gaussian density function over the whole real line.") | |
| # Evaluating the Gaussian Integral over the Entire Real Line | |
| The integral of the Gaussian density function over the whole real line is a fundamental result in mathematics and | |
| statistics: | |
| $$\int_{-\infty}^{\infty} e^{-x^2/2} dx = \sqrt{2\pi}$$ |
vjcitn
/ measure_cnn.R
Created
May 11, 2026 10:48
use macmon to develop report on GPU usage on m4 mac
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| library(littleDeep) | |
| library(processx) | |
| tf = tempfile() | |
| fstr = paste0(">>", tf) | |
| #file.create(tf) | |
| basecmd = sprintf("/Users/vincentcarey/INSTRUMENTATION/macmon/target/release/macmon") | |
| pp = process$new(basecmd, c("pipe"), stdout=fstr) | |
| suppress_keras_warnings() | |
| r1 = run_cifar100(nEpochs=3) | |
| pp$kill() |
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| #> dput(dev) | |
| alogit = function(x) exp(x)/(1+exp(x)) | |
| dev = function (y, x) | |
| function(b) { | |
| phat = alogit(x %*% b) | |
| -2 * sum(y * log(phat) + (1 - y) * (log(1 - phat))) | |
| } | |
| Y = 1*(iris$Species == "virginica") | |
| X = data.matrix(cbind(1., iris[,1:4])) |
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| available_sdio produces: | |
| > reticulate::py_last_error() | |
| ── Python Exception Message ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
| Traceback (most recent call last): | |
| File "C:\Users\stvjc\AppData\Local\R\win-library\4.6\reticulate\python\rpytools\loader.py", line 122, in _find_and_load_hook | |
| return _run_hook(name, _hook) | |
| ^^^^^^^^^^^^^^^^^^^^^^ | |
| File "C:\Users\stvjc\AppData\Local\R\win-library\4.6\reticulate\python\rpytools\loader.py", line 96, in _run_hook | |
| module = hook() |
vjcitn
/ dogencode.R
Created
March 12, 2026 10:31
Explore GenomicState+txdbmaker functions for working with Gencode V49
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| library(GenomicState) | |
| library(RSQLite) | |
| library(txdbmaker) | |
| hgenc49 = gencode_txdb( | |
| version = "49", | |
| genome = c("hg38"), | |
| chrs = paste0("chr", c(seq_len(22), "X", "Y", "M")) | |
| ) | |
| hgenc49$conn # 'path' is empty | |
| md = dbGetQuery(hgenc49$conn, "select * from metadata") # lacks 'Resource URL' record in metadata |
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| 8/51 [install-miniconda] | |
| trying URL 'https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh' | |
| Content type 'application/octet-stream' length 105158150 bytes (100.3 MB) | |
| ================================================== | |
| downloaded 100.3 MB | |
| PREFIX=/root/.local/share/r-miniconda | |
| Unpacking bootstrapper... | |
| Unpacking payload... | |
| Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2 |
vjcitn
/ gencodeError.txt
Last active
January 9, 2026 13:42
traceback for using GENCODE in bioconductor; need CENTREannotation attached to avoid this
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| > query(ah, c("GENCODE", "human")) | |
| AnnotationHub with 87 records | |
| # snapshotDate(): 2025-10-29 | |
| # $dataprovider: GENCODE, Gencode, BroadInstitute, ENCODE | |
| # $species: Homo sapiens | |
| # $rdataclass: GRanges, list, TxDb, SQLiteConnection | |
| # additional mcols(): taxonomyid, genome, description, | |
| # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, | |
| # rdatapath, sourceurl, sourcetype | |
| # retrieve records with, e.g., 'object[["AH49010"]]' |
vjcitn
/ bedarray.R
Last active
November 13, 2025 18:33
DelayedArray back end for plink2 bed, before I learned about BEDMatrix
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| library(DelayedArray) | |
| setClass("plBedSeed", | |
| contains="Array", | |
| slots = c( | |
| dim = "integer", | |
| bedreaderRef = "ANY", | |
| dimnames = "list" | |
| ) | |
| ) |
vjcitn
/ make1zip.R
Last active
November 10, 2025 22:09
create one zip file for a source package on windows
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| make1zip = function(pname, target="zips322") { | |
| if (!dir.exists(target)) dir.create(target) | |
| target = file.path(getwd(), target) | |
| ins = try(BiocManager::install(pname, ask=FALSE, update=FALSE, type="binary", | |
| dependencies=TRUE, force=TRUE)) # acquire dependencies as needed | |
| if (inherits(ins, "try-error")) stop(sprintf("can't install %s with BiocManager", pname)) | |
| #real_inst = try(install.packages(pname, type="source", repos=NULL)) # this uses native windows build tools from Rtools | |
| bpath = pkgbuild::build(pname) | |
| if (inherits(bpath, "try-error")) stop(sprintf("can't build %s from source", pname)) | |
| install.packages(bpath, type="source", repos=NULL) |
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| library(BiocPkgTools) | |
| all322 = biocPkgList(version="3.22", repo="BioCsoft")$Package | |
| library(BiocBuildTools) # from github vjcitn | |
| set322=PackageSet(all322, biocversion="3.22", branchname="RELEASE_3_22") | |
| dir.create("srcs_322") | |
| populate_local_gits(set322, gitspath="srcs_322") |
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