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Merge branch '3.4'
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@jonclayden
jonclayden committed May 10, 2024
2 parents ddbcfe3 + f7a051d commit 0080291
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Showing 10 changed files with 18 additions and 13 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/docker.yaml
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Expand Up @@ -19,7 +19,7 @@ jobs:

steps:
- name: Check out code
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
submodules: true

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3 changes: 1 addition & 2 deletions Makefile
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Expand Up @@ -95,7 +95,6 @@ clean:
distclean: clean
@rm -f lib/.timestamp
@rm -f bin/exec/tractor src/tractor.o src/build.log install.log
@rm -f tractor.track/config.log tractor.track/config.status tractor.track/src/Makevars tractor.track/src/config.h

test:
@cd tests && $(MAKE) run-tests R=$(R)
Expand All @@ -110,7 +109,7 @@ utest: lib/R/tinytest lib/R/oro.nifti lib/R/igraph
deeptest: utest test

create-md5:
@$(GIT) ls-files | grep -v -e '^lib/' -e '^md5.txt' -e '\.git' | xargs $(MD5) -r >md5.txt
@$(GIT) ls-files | grep -v -e '^lib/' -e '^md5\.txt' -e '\.git' -e 'tests/data/images' | xargs $(MD5) -r >md5.txt

check-md5:
@mkdir -p tmp
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2 changes: 1 addition & 1 deletion VERSION
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@@ -1 +1 @@
3.4.2
3.4.3
2 changes: 1 addition & 1 deletion lib/RNifti
Submodule RNifti updated 8 files
+2 −2 DESCRIPTION
+7 −0 NEWS
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+3 −3 inst/include/RNifti/NiftiImage_print.h
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+7 −7 src/niftilib/nifti2_io.c
2 changes: 1 addition & 1 deletion lib/Rcpp
Submodule Rcpp updated 45 files
+1 −0 .Rbuildignore
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+213 −0 ChangeLog
+3 −2 DESCRIPTION
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+9 −1 R/RcppLdpath.R
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+1 −1 man/getRcppVersion.Rd
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+1 −0 src/date.cpp
+ − vignettes/pdf/Rcpp-FAQ.pdf
+ − vignettes/pdf/Rcpp-attributes.pdf
+ − vignettes/pdf/Rcpp-extending.pdf
+ − vignettes/pdf/Rcpp-introduction.pdf
+ − vignettes/pdf/Rcpp-jss-2011.pdf
+ − vignettes/pdf/Rcpp-libraries.pdf
+ − vignettes/pdf/Rcpp-modules.pdf
+ − vignettes/pdf/Rcpp-package.pdf
+ − vignettes/pdf/Rcpp-quickref.pdf
+ − vignettes/pdf/Rcpp-sugar.pdf
+104 −104 vignettes/rmd/Rcpp-FAQ.Rmd
+1 −1 vignettes/rmd/Rcpp-introduction.Rmd
+67 −50 vignettes/rmd/Rcpp.bib
2 changes: 1 addition & 1 deletion lib/jsonlite
Submodule jsonlite updated 63 files
+1 −1 .github/workflows/R-CMD-check.yaml
+79 −0 .github/workflows/rhub.yaml
+1 −1 COPYING
+4 −3 DESCRIPTION
+1 −0 NAMESPACE
+15 −0 NEWS
+5 −0 R/apply_by_pages.R
+1 −1 R/asJSON.AAAgeneric.R
+5 −0 R/asJSON.vctrs.R
+4 −4 R/simplify.R
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+0 −18 revdep/cran.md
+0 −78 revdep/failures.md
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+0 −38 revdep/problems.md
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+30 −30 tests/testthat/test-toJSON-POSIXt.R
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+6 −6 tests/testthat/test-toJSON-matrix.R
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+3 −3 tests/testthat/test-toJSON-raw.R
+20 −20 tests/testthat/test-toJSON-zerovec.R
+0 −9 tidy.R
2 changes: 1 addition & 1 deletion lib/yaml
Submodule yaml updated 11 files
+4 −4 DESCRIPTION
+1 −1 LICENSE
+10 −8 MD5
+1 −1 NAMESPACE
+5 −0 R/verbatim_logical.R
+3 −0 inst/CHANGELOG
+1 −6 man/as.yaml.Rd
+43 −0 man/verbatim_logical.Rd
+1 −1 src/dumper.c
+1 −1 src/r_emit.c
+1 −1 src/r_parse.c
8 changes: 4 additions & 4 deletions md5.txt
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Expand Up @@ -6,9 +6,9 @@ d654c028827567e62ddbde4fa5b100d8 CITATION.cff
a5391c7555bd912343ae34a4ebf8ba89 Dockerfile
6df8bfd02fd1dd8e238c7525eccbb8f5 INSTALL.md
10b634d9e14144c8b6aa3562b4877ede LICENSE
557f2c428f5ce3e7848ee9337e537ad0 Makefile
54caee9bdcb6278b7b434e4e5990e55c Makefile
4f35cdd9c87b6d7b766823a4ee3a9a59 README.md
a04a1335aea3f7a6ce9e0595b404f7c7 VERSION
91333fc1f54ea20888ca61e7f0c63c23 VERSION
f13a73bd17fbe0f54870413c386c301a bin/extra/tractor_Rinstall
5493da6482c836e47652578590daa718 bin/furrow
87c38f3730a914abe1738c8c52679e4c bin/plough
Expand All @@ -21,7 +21,7 @@ a09a862f22f56b5a661c3d9ad22d2c94 share/doc/TractoR-for-R-users.html
ce088d53ef9561c4dd85577f4c4e10ba share/doc/assets/prism.css
cdca90be556c2e5f8dfb1482e0fc09e9 share/doc/assets/prism.js
6b43348eebd7eec7694595976f84b74e share/doc/assets/style.css
31c54dcf47005f494690538d7810e274 share/doc/changelog.html
402e6f86230d1f36ee8c497e6b014cbb share/doc/changelog.html
e64c8bf71e4b734c86afe8a7ccfe7d22 share/doc/connectivity-graphs.html
f8d1b523df854498067db69fcc1a8b61 share/doc/conventions.html
a819a5c58a57f1f317888c4037b82a7b share/doc/diffusion-processing.html
Expand All @@ -33,7 +33,7 @@ cd8cec91833ffa792d4ad33729f8acbf share/doc/graph-brain.png
fd0b3ec2dc56fcc4ad96953aab138c0e share/doc/graph-matrix.png
aa9d14c499979d80fdff28dfbf0db5d5 share/doc/guidelines-for-contributors.html
3c11235b2bef0c0b296fc0482a9d6e4b share/doc/home.html
709b9f6c966bf73c06b475a395307e73 share/doc/install.html
3962c2eb60fb5e0fa5b3e1fec961fbe4 share/doc/install.html
f200f315d515320dc4e8c1fe13f52a59 share/doc/nitrc.png
614b517b59fcee58ec3e0365c5db0d47 share/doc/paper/index.html
b34a574652afa4baf8b594b9262b8c4c share/doc/principal-directions.png
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6 changes: 6 additions & 0 deletions share/doc/changelog.html
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Expand Up @@ -48,6 +48,12 @@ <h1>Changelog</h1>

<p>The significant user-visible changes in each release of TractoR are documented below.</p>

<h2 id="343-2024-05-08">3.4.3 (2024-05-08)</h2>

<ul>
<li>Dependency packages <code>jsonlite</code>, <code>yaml</code>, <code>Rcpp</code> and <code>RNifti</code> have been updated for compatibility with the now-released R 4.4.0.</li>
</ul>

<h2 id="342-2024-03-01">3.4.2 (2024-03-01)</h2>

<ul>
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2 changes: 1 addition & 1 deletion share/doc/install.html
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Expand Up @@ -57,7 +57,7 @@ <h2 id="system-requirements">System requirements</h2>
<h2 id="downloads">Downloads</h2>

<div id="download-box">
<p>The latest version of TractoR is <span id="version">v3.4.1</span>.</p>
<p>The latest version of TractoR is <span id="version">v3.4.2</span>.</p>
<img src="download.png" alt="Download icon">
<p>Download <a href="#" onclick="gtag('event','download_tarball'); window.location.href='http://www.tractor-mri.org.uk/tractor.tar.gz'">tractor.tar.gz</a> or <a href="#" onclick="gtag('event','download_zipball'); window.location.href='http://www.tractor-mri.org.uk/tractor.zip'">tractor.zip</a>.</p>
</div>
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