From e11543b8d3ac2c14e43dc77a6b1b7ca6d64ee15d Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 17 Sep 2025 15:05:08 +0100 Subject: [PATCH 1/5] noLD note --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index 5c94ffc1..d728f56e 100644 --- a/README.md +++ b/README.md @@ -73,3 +73,10 @@ The code here is organised as: mitigating disclosure risk in a multi-site federated analysis platform.” _Bioinformatics Advances_, *5*(1), 1-21. . +> **_Note:_** Apple Mx architecture users, please be aware that there are some numerical limitations on this platform, which leads to unexpected results when using base R packages, like stats​. +> +> x <- c(0, 3, 7) +> 1 - cor(x, x)​ +> +> The above should result in a value of zero. +> _Also see:_ https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f and this was the bug report that I had opened: https://bugs.r-project.org/show_bug.cgi?id=18941 From 5de165b776716a5cc99c1575269f64202ebff2b5 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 17 Sep 2025 15:24:26 +0100 Subject: [PATCH 2/5] Reformat 'note' --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index d728f56e..c09ca0a7 100644 --- a/README.md +++ b/README.md @@ -76,7 +76,9 @@ The code here is organised as: > **_Note:_** Apple Mx architecture users, please be aware that there are some numerical limitations on this platform, which leads to unexpected results when using base R packages, like stats​. > > x <- c(0, 3, 7) +> > 1 - cor(x, x)​ > > The above should result in a value of zero. -> _Also see:_ https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f and this was the bug report that I had opened: https://bugs.r-project.org/show_bug.cgi?id=18941 +> +> _Also see:_ For some details https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f and the bug report: https://bugs.r-project.org/show_bug.cgi?id=18941 From 19a21a61a8dc6450d64bc4a630ea0cb62405213c Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 17 Sep 2025 15:28:37 +0100 Subject: [PATCH 3/5] Improved note content --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c09ca0a7..c82341b5 100644 --- a/README.md +++ b/README.md @@ -81,4 +81,4 @@ The code here is organised as: > > The above should result in a value of zero. > -> _Also see:_ For some details https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f and the bug report: https://bugs.r-project.org/show_bug.cgi?id=18941 +> _Also See:_ For more details see https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f and the bug report: https://bugs.r-project.org/show_bug.cgi?id=18941 From 6a236fe82c6195d4920d563cce4f7348de649e0a Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 17 Sep 2025 16:14:00 +0100 Subject: [PATCH 4/5] Updates including noLD note --- docs/authors.html | 3 +-- docs/index.html | 15 +++++++++++---- docs/pkgdown.yml | 4 ++-- 3 files changed, 14 insertions(+), 8 deletions(-) diff --git a/docs/authors.html b/docs/authors.html index 123fdbbe..ed00c664 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -104,14 +104,13 @@

Citation

-

Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà-Montagut X, Wheater S (2025). +

Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà-Montagut X, Wheater S (????). dsBaseClient: 'DataSHIELD' Client Side Base Functions. R package version 6.3.4. 

@Manual{,
   title = {dsBaseClient: 'DataSHIELD' Client Side Base Functions},
   author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier Escribà-Montagut and Stuart Wheater},
-  year = {2025},
   note = {R package version 6.3.4},
 }

Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I, Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry I, Peters A, Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier I, Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). diff --git a/docs/index.html b/docs/index.html index 9e70df5c..cc91e149 100644 --- a/docs/index.html +++ b/docs/index.html @@ -88,20 +88,20 @@

About - + Location What is it? - + obiba CRAN Where you probably should install DataSHIELD from. - + releases Stable releases. - + master branch Mostly in sync with the latest release, changes rarely. @@ -115,6 +115,13 @@

Referenceshttps://doi.org/10.1093/ije/dyu188.

[3] Wilson R, W. Butters O, Avraam D, Baker J, Tedds J, Turner A, Murtagh M, R. Burton P (2017). “DataSHIELD – New Directions and Dimensions.” Data Science Journal, 16(21), 1-21. https://doi.org/10.5334/dsj-2017-021.

[4] Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan A, Murtagh M, Nestor M, Nybo Andersen A, Parker S, Pinot de Moira A, Schwarz F, Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). “DataSHIELD: mitigating disclosure risk in a multi-site federated analysis platform.” Bioinformatics Advances, 5(1), 1-21. https://doi.org/10.1093/bioadv/vbaf046.

+
+

Note: Apple Mx architecture users, please be aware that there are some numerical limitations on this platform, which leads to unexpected results when using base R packages, like stats​.

+

x <- c(0, 3, 7)

+

1 - cor(x, x)​

+

The above should result in a value of zero.

+

Also See: For more details see https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f and the bug report: https://bugs.r-project.org/show_bug.cgi?id=18941

+
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 97ec34a7..ee4120e3 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ -pandoc: '3.4' +pandoc: 3.1.3 pkgdown: 2.1.3 pkgdown_sha: ~ articles: {} -last_built: 2025-09-17T09:27Z +last_built: 2025-09-17T15:10Z From 7718af08ea7bb1689d21d683a70e57cedae3b67a Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 17 Sep 2025 17:12:44 +0100 Subject: [PATCH 5/5] Update authors.html Keep year for `dsBase` citation as 2025, instead of ???? --- docs/authors.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/authors.html b/docs/authors.html index ed00c664..177847f6 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -104,7 +104,7 @@

Citation

-

Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà-Montagut X, Wheater S (????). +

Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà-Montagut X, Wheater S (2025). dsBaseClient: 'DataSHIELD' Client Side Base Functions. R package version 6.3.4.