Split call_block into a function block_params #1870
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…o get a data.frame of parameters if looped
# remotes::install_github('muschellij2/knitr')
library(knitr)
knit_df = function(file) {
x = xfun::read_utf8(file)
on.exit(knitr::knit_code$restore(), add = TRUE)
res = knitr:::split_file(x, patterns = knitr::all_patterns$md)
classes = sapply(res, attr, "class")
blocks = res[classes %in% "block"]
params = lapply(blocks, function(el) {
if (attr(el, "class") %in% "block") {
knitr:::block_params(el, verbose = FALSE)
} else {
NULL
}
})
df = lapply(params, function(x) {
if (!is.null(x)) {
keep_names = c("eval", "echo", "engine",
"label", "code", "hash", "cache",
"cache.path", "cache.vars",
"cache.lazy", "fig.path", "fig.ext",
"fig.env", "error", "warning", "message",
"include", "params.src")
x$code = paste(x$code, collapse = "\n")
x = lapply(keep_names, function(r) {
xx = x[[r]]
if (is.null(xx)) {
xx = NA
}
xx
})
names(x) = keep_names
as.data.frame(x[keep_names])
} else {
NULL
}
})
df = do.call("rbind", df)
return(df)
}
tfile = tempfile(fileext = ".Rmd")
curl::curl_download(
"https://raw.githubusercontent.com/muschellij2/neuroc/master/brain_extraction/index.Rmd",
destfile = tfile)
res = knit_df(tfile)
head(res, 10)
#> eval echo engine label
#> 1 TRUE TRUE R setup
#> 2 FALSE TRUE R unnamed-chunk-1
#> 3 TRUE TRUE R data
#> 4 TRUE TRUE R t1_plot
#> 5 TRUE TRUE R t1_naive_ss
#> 6 TRUE TRUE R t1_naive_plot
#> 7 TRUE TRUE R t1_ss
#> 8 TRUE TRUE R t1_ss_plot
#> 9 TRUE TRUE R t1_ss_plot2
#> 10 TRUE TRUE R t1_ss_red
#> code
#> 1 library(kirby21.fmri)\nlibrary(kirby21.base)\nlibrary(dplyr)\nlibrary(fslr)\nlibrary(neurobase)\nlibrary(ANTsR)\nlibrary(R.utils)\nlibrary(RColorBrewer)\nlibrary(matrixStats)\nlibrary(ggplot2)\nlibrary(reshape2)\nlibrary(animation)\nlibrary(zoo)\nknitr::opts_chunk$set(echo = TRUE, cache = TRUE, comment = "",\n cache.path = "index_cache/html/")
#> 2 source("https://neuroconductor.org/neurocLite.R")\npackages = installed.packages()\npackages = packages[, "Package"]\nif (!"kirby21.base" %in% packages) {\n neuroc_install("kirby21.base") \n}\nif (!"kirby21.t1" %in% packages) {\n neuroc_install("kirby21.t1") \n}
#> 3 library(kirby21.t1)\nlibrary(kirby21.base)\nfnames = get_image_filenames_df(ids = 113, \n modalities = c("T1"), \n visits = c(1),\n long = FALSE)\nt1_fname = fnames$T1[1]
#> 4 t1 = readnii(t1_fname)\northo2(t1)\nrm(list = "t1")
#> 5 library(fslr)\noutfile = nii.stub(t1_fname, bn = TRUE)\noutfile = paste0(outfile, "_SS_Naive.nii.gz")\nif (!file.exists(outfile)) {\n ss_naive = fslbet(infile = t1_fname, outfile = outfile)\n} else {\n ss_naive = readnii(outfile)\n}
#> 6 ortho2(ss_naive)
#> 7 outfile = nii.stub(t1_fname, bn = TRUE)\noutfile = paste0(outfile, "_SS.nii.gz")\nif (!file.exists(outfile)) {\n ss = extrantsr::fslbet_robust(t1_fname, \n remover = "double_remove_neck",\n outfile = outfile)\n} else {\n ss = readnii(outfile)\n}
#> 8 ortho2(ss)
#> 9 alpha = function(col, alpha = 1) {\n cols = t(col2rgb(col, alpha = FALSE)/255)\n rgb(cols, alpha = alpha)\n} \northo2(t1_fname, ss > 0, col.y = alpha("red", 0.5))
#> 10 ss_red = dropEmptyImageDimensions(ss)\northo2(ss_red)
#> hash
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 reprex_reprex_cache/markdown_strict/t1_plot_1237e2a884712bffa363745c73aaa7f5
#> 5 <NA>
#> 6 reprex_reprex_cache/markdown_strict/t1_naive_plot_2bcd17d374dad557a2c9b5a588b7f9ad
#> 7 <NA>
#> 8 reprex_reprex_cache/markdown_strict/t1_ss_plot_cb7fa3ba47fae618f174f2bf40e2e415
#> 9 reprex_reprex_cache/markdown_strict/t1_ss_plot2_c6fa4be8d26d1758967f5541180b9e81
#> 10 <NA>
#> cache cache.path cache.vars cache.lazy
#> 1 0 reprex_reprex_cache/markdown_strict/ NA TRUE
#> 2 0 reprex_reprex_cache/markdown_strict/ NA TRUE
#> 3 0 reprex_reprex_cache/markdown_strict/ NA TRUE
#> 4 3 reprex_reprex_cache/markdown_strict/ NA TRUE
#> 5 0 reprex_reprex_cache/markdown_strict/ NA TRUE
#> 6 3 reprex_reprex_cache/markdown_strict/ NA TRUE
#> 7 0 reprex_reprex_cache/markdown_strict/ NA TRUE
#> 8 3 reprex_reprex_cache/markdown_strict/ NA TRUE
#> 9 3 reprex_reprex_cache/markdown_strict/ NA TRUE
#> 10 0 reprex_reprex_cache/markdown_strict/ NA TRUE
#> fig.path fig.ext fig.env error warning
#> 1 reprex_reprex_files/figure-markdown_strict/ NA figure TRUE TRUE
#> 2 reprex_reprex_files/figure-markdown_strict/ NA figure TRUE TRUE
#> 3 reprex_reprex_files/figure-markdown_strict/ NA figure TRUE TRUE
#> 4 reprex_reprex_files/figure-markdown_strict/ NA figure TRUE TRUE
#> 5 reprex_reprex_files/figure-markdown_strict/ NA figure TRUE TRUE
#> 6 reprex_reprex_files/figure-markdown_strict/ NA figure TRUE TRUE
#> 7 reprex_reprex_files/figure-markdown_strict/ NA figure TRUE TRUE
#> 8 reprex_reprex_files/figure-markdown_strict/ NA figure TRUE TRUE
#> 9 reprex_reprex_files/figure-markdown_strict/ NA figure TRUE TRUE
#> 10 reprex_reprex_files/figure-markdown_strict/ NA figure TRUE TRUE
#> message include params.src
#> 1 TRUE FALSE setup, include=FALSE
#> 2 TRUE TRUE eval = FALSE
#> 3 TRUE TRUE data
#> 4 TRUE TRUE t1_plot, cache = TRUE
#> 5 TRUE TRUE t1_naive_ss, cache = FALSE
#> 6 TRUE TRUE t1_naive_plot, cache = TRUE
#> 7 TRUE TRUE t1_ss, cache = FALSE
#> 8 TRUE TRUE t1_ss_plot, cache = TRUE
#> 9 TRUE TRUE t1_ss_plot2, cache = TRUE
#> 10 TRUE TRUE t1_ss_red, cache = FALSECreated on 2020-06-28 by the reprex package (v0.3.0) |
yihui
requested changes
Jul 23, 2020
|
And |
|
I think those changes were from a merge upstream, but I will delete.
Best,
John
…On Thu, Jul 23, 2020 at 4:13 PM Yihui Xie ***@***.***> wrote:
And R CMD check failed on Travis. Please also make sure the PR passes the
checks (or state it if the failure is irrelevant to your PR).
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#1870 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/AAIGPLTSIQJM5KONJBJD5CLR5CKWPANCNFSM4OJOFBCA>
.
|
|
I don't know what this failure really is - it seems as though it's in the examples, but I'm unsure if that's anything of my code. |
|
Examples 087 and 112 failed: https://travis-ci.com/github/yihui/knitr/jobs/369838241#L3167-L3168 You may try reproduce locally and fix the errors: https://github.com/yihui/knitr-examples |
|
|
|
Seems odd - why would that not be triggered on |
yihui
reviewed
Apr 8, 2021
There was a problem hiding this comment.
All checks on all platforms are still failing (with the same error), e.g.,
https://github.com/yihui/knitr/pull/1870/checks?check_run_id=2227943814
https://github.com/yihui/knitr/pull/1870/checks?check_run_id=2227943929
|
I don't have time this week to review, but maybe next |
|
That's okay. I plan to make a CRAN release in the next few days. If this PR won't catch the next release, I can place it in a future release. Thanks! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
call_blockdoes all the extraction of the parameters necessary, but executes the block. Regarding our email of getting adata.frameof parameters/hash/etc, I think that is what we'd need. I splitcall_blockinto ablock_paramsfunction that extracts the parameters, and then callblock_paramsincall_block.