From d6b10ae09c3913b94b415e2c7037123d6d8eb423 Mon Sep 17 00:00:00 2001 From: august Date: Tue, 5 Feb 2019 12:44:48 -0500 Subject: [PATCH 1/5] Update paper.md --- paper/paper.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index 9e4b024..6178910 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -16,8 +16,8 @@ affiliations: name: Center for Computation and Visualization, Brown University, Providence, Rhode Island, United States of America - index: 2 name: Center for Computational Biology of Human Disease, Brown University, Providence, Rhode Island, United States of America -- date: 5 February 2019 -- bibliography: paper.bib +date: 5 February 2019 +bibliography: paper.bib --- Summary From aa35c057c735f3e9f40b056750a7a1499fd753b3 Mon Sep 17 00:00:00 2001 From: august Date: Tue, 5 Feb 2019 12:48:20 -0500 Subject: [PATCH 2/5] Update paper.md --- paper/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paper/paper.md b/paper/paper.md index 6178910..7e98468 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -3,7 +3,7 @@ title: 'RSeqAn: Headers and wrappers for the SeqAn library in R' author: - August Guang authors: -- affiliation: 1,2 +- affiliation: "1,2" name: August Guang orcid: 0000-0003-0872-7098 tags: From 33577b2621ecd08f55fe29e1f7c6d1fe72bf80d9 Mon Sep 17 00:00:00 2001 From: august Date: Tue, 5 Feb 2019 13:01:18 -0500 Subject: [PATCH 3/5] Update README.md --- README.md | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 3b4b955..1ed6cd4 100644 --- a/README.md +++ b/README.md @@ -22,13 +22,19 @@ Don't forget to set the C++14 compiler flags if you do this! ## Installation -We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html). Instructions are provided on their page. +We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html), especially if you are running R on Windows. Instructions are provided on their page. -If you have `devtools`, then the development version can be installed from here by running: +Version 1.3.1 can also be installed [through Bioconductor](http://bioconductor.org/packages/devel/bioc/html/RSeqAn.html), downloaded as [a tagged release](https://github.com/compbiocore/RSeqAn/releases/tag/v1.3.1), or installed with `devtools` by running: ```r -devtools::install_github("compbiocore/RSeqAn") +devtools::install_github("compbiocore/RSeqAn", ref="v1.3.1") ``` -The development version contains `Rcpp::as` and `Rcpp::wrap` functions for `CharString`. +This version contains `Rcpp::as` and `Rcpp::wrap` functions for `CharString` and is the one submitted to the [Journal of Open Source Software](https://joss.theoj.org/). + +The development version can be installed with `devtools` by running: +```r +devtools::install_github("compbiocore/RSeqAn", ref="devel") +``` +This version contains additional wrappers, though we cannot guarantee that they will work for you. ## Author From 1a09758e1ca35e0e21780a3cf4313a5e97349ac1 Mon Sep 17 00:00:00 2001 From: august Date: Tue, 5 Feb 2019 13:02:01 -0500 Subject: [PATCH 4/5] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 1ed6cd4..c501733 100644 --- a/README.md +++ b/README.md @@ -22,15 +22,15 @@ Don't forget to set the C++14 compiler flags if you do this! ## Installation -We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html), especially if you are running R on Windows. Instructions are provided on their page. + * We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html), especially if you are running R on Windows. Instructions are provided on their page. -Version 1.3.1 can also be installed [through Bioconductor](http://bioconductor.org/packages/devel/bioc/html/RSeqAn.html), downloaded as [a tagged release](https://github.com/compbiocore/RSeqAn/releases/tag/v1.3.1), or installed with `devtools` by running: + * Version 1.3.1 can also be installed [through Bioconductor](http://bioconductor.org/packages/devel/bioc/html/RSeqAn.html), downloaded as [a tagged release](https://github.com/compbiocore/RSeqAn/releases/tag/v1.3.1), or installed with `devtools` by running: ```r devtools::install_github("compbiocore/RSeqAn", ref="v1.3.1") ``` This version contains `Rcpp::as` and `Rcpp::wrap` functions for `CharString` and is the one submitted to the [Journal of Open Source Software](https://joss.theoj.org/). -The development version can be installed with `devtools` by running: + * The development version can be installed with `devtools` by running: ```r devtools::install_github("compbiocore/RSeqAn", ref="devel") ``` From a7a89c3fa3c425a9a47d213d32b939554c0bc98f Mon Sep 17 00:00:00 2001 From: august Date: Tue, 5 Feb 2019 13:08:50 -0500 Subject: [PATCH 5/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c501733..be92349 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ Don't forget to set the C++14 compiler flags if you do this! * We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html), especially if you are running R on Windows. Instructions are provided on their page. - * Version 1.3.1 can also be installed [through Bioconductor](http://bioconductor.org/packages/devel/bioc/html/RSeqAn.html), downloaded as [a tagged release](https://github.com/compbiocore/RSeqAn/releases/tag/v1.3.1), or installed with `devtools` by running: + * Version 1.3.1 can also be installed [through Bioconductor](http://bioconductor.org/packages/devel/bioc/html/RSeqAn.html) (for now, Bioconductor has a separate release cycle), downloaded as [a tagged release](https://github.com/compbiocore/RSeqAn/releases/tag/v1.3.1), or installed with `devtools` by running: ```r devtools::install_github("compbiocore/RSeqAn", ref="v1.3.1") ```