GNU bug report logs - #62441
[patch] gnu: Add r-ctrialsgov, r-jsonify, r-nodbi, r-ctrdata.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [patch] gnu: Add r-ctrialsgov, r-jsonify, r-nodbi, r-ctrdata.
Date: Sat, 25 Mar 2023 11:24:22 +0100

* gnu/packages/cran.scm (r-ctrialsgov, r-jsonify, r-nodbi, r-ctrdata): 
New variables.

Message #8 received at 62441 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62441 <at> debbugs.gnu.org>
Subject: [PATCH 3/4] gnu: Add r-nodbi.
Date: Sat, 25 Mar 2023 18:45:54 +0100

* gnu/packages/cran.scm (r-nodbi): New variable.
---
 gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 034dd0869a..9b314bae43 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -12275,6 +12275,33 @@ (define-public r-sjmisc
 tidyverse workflow.")
     (license license:gpl3)))
 
+(define-public r-nodbi
+  (package
+    (name "r-nodbi")
+    (version "0.9.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "nodbi" version))
+       (sha256
+        (base32 "1hn0wy2ry9l3wwqrshmf82cxigkm16wycwprv458bcvb5k6ayy5m"))))
+    (properties `((upstream-name . "nodbi")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-dbi
+           r-jqr
+           r-jsonify
+           r-jsonlite
+           r-stringi
+           r-uuid))
+    (home-page "https://docs.ropensci.org/nodbi/")
+    (synopsis "NoSQL database connector")
+    (description
+     "The nodbi package aims to simplified document database access and
+manipulation, by providing a common API across supported NoSQL databases
+Elasticsearch, CouchDB, MongoDB as well as SQLite/JSON1, PostgreSQL, and DuckDB.")
+    (license license:expat)))
+
 (define-public r-nortest
   (package
     (name "r-nortest")
-- 
2.39.2

Message #11 received at 62441 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62441 <at> debbugs.gnu.org>
Subject: [PATCH 1/4] gnu: Add r-ctrialsgov.
Date: Sat, 25 Mar 2023 18:45:52 +0100

* gnu/packages/cran.scm (r-ctrialsgov): New variable.
---
 gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a36c845479..a3590fe9cd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -396,6 +396,43 @@ (define-public r-cplm
 comparison tool involving zero-inflated and highly skewed distributions.")
     (license license:gpl2+)))
 
+(define-public r-ctrialsgov
+  (package
+    (name "r-ctrialsgov")
+    (version "0.2.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ctrialsgov" version))
+       (sha256
+        (base32 "0hdh1fdfaja8amf7fkvk1c6yif703132bvacq0j9pk5jr97czgpw"))))
+    (properties `((upstream-name . "ctrialsgov")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-dbi
+           r-dplyr
+           r-ggplot2
+           r-htmlwidgets
+           r-lubridate
+           r-matrix
+           r-plotly
+           r-purrr
+           r-rlang
+           r-stringi
+           r-tibble))
+    (native-inputs (list r-knitr))
+    (home-page "https://cran.r-project.org/package=ctrialsgov")
+    (synopsis
+     "Query data from U.S. National Library of Medicine's Clinical trials database")
+    (description
+     "The ctrialsgov package implements a series of tools which create and query
+database from the United States National Library of Medicine's Clinical trials
+database @url{https://clinicaltrials.gov/}.  Functions provide access a variety
+of techniques for searching the data using range queries, categorical filtering,
+and by searching for full-text keywords.  Minimal graphical tools are also
+provided for interactively exploring the constructed data.")
+    (license license:expat)))
+
 (define-public r-curry
   (package
     (name "r-curry")

base-commit: de84b24613afa4020f3f0553dad8e39a78d1f92c
-- 
2.39.2

Message #14 received at 62441 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62441 <at> debbugs.gnu.org>
Subject: [PATCH 2/4] gnu: Add r-jsonify.
Date: Sat, 25 Mar 2023 18:45:53 +0100

* gnu/packages/cran.scm (r-jsonify): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a3590fe9cd..034dd0869a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3309,6 +3309,27 @@ (define-public r-jsonlite
 in systems and applications.")
     (license license:expat)))
 
+(define-public r-jsonify
+  (package
+    (name "r-jsonify")
+    (version "1.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "jsonify" version))
+       (sha256
+        (base32 "0bxgyj5b1hnijq5315g050giixy4k5mjz2zdx8yil0igb5ifji9p"))))
+    (properties `((upstream-name . "jsonify")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rapidjsonr r-rcpp))
+    (native-inputs (list r-knitr))
+    (home-page "https://cran.r-project.org/package=jsonify")
+    (synopsis "Convert between R objects and Javascript object notation (JSON)")
+    (description
+     "The jsonify package helps with the conversions between R objects and
+@acronym{JSON, Javascript Object Notation} using the rapidjsonr library.")
+    (license license:expat)))
+
 (define-public r-servr
   (package
     (name "r-servr")
-- 
2.39.2

Message #17 received at 62441 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62441 <at> debbugs.gnu.org>
Subject: [PATCH 4/4] gnu: Add r-ctrdata.
Date: Sat, 25 Mar 2023 18:45:55 +0100

* gnu/packages/cran.scm (r-ctrdata): New variable.
---
 gnu/packages/cran.scm | 46 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9b314bae43..6e70dd134a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -97,6 +97,7 @@ (define-module (gnu packages cran)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages pdf)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages php)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)  ;libsndfile
   #:use-module (gnu packages protobuf)
@@ -396,6 +397,51 @@ (define-public r-cplm
 comparison tool involving zero-inflated and highly skewed distributions.")
     (license license:gpl2+)))
 
+(define-public r-ctrdata
+  (package
+    (name "r-ctrdata")
+    (version "1.11.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ctrdata" version))
+       (sha256
+        (base32 "076v3bll8s6m61wcbwgrgrm34g0wa7gsc90mbwxwap1xfxyzjjsg"))))
+    (properties `((upstream-name . "ctrdata")))
+    (build-system r-build-system)
+    (inputs
+     (list coreutils
+           perl
+           php
+           sed))
+    (propagated-inputs
+     (list r-clipr
+           r-curl
+           r-dplyr
+           r-httr
+           r-jsonlite
+           r-lubridate
+           r-nodbi
+           r-rvest
+           r-stringi
+           r-xml2))
+    (native-inputs (list r-r-rsp))
+    (home-page "https://cran.r-project.org/package=ctrdata")
+    (synopsis "Retrieve and analyze clinical trials in public registers")
+    (description
+     "This package provides a system for querying, retrieving and analyzing
+protocol- and results-related information on clinical trials from three public
+registers, the @acronym{EUCTR, European Union Clinical Trials Register} @url{
+https://www.clinicaltrialsregister.eu/}, @acronym{CTGOV, ClinicalTrials.gov}
+@url{https://clinicaltrials.gov/} and the @acronym{ISRCTN, International Clinical
+Trials Registry Platform} @url{https://www.isrctn.com/}.  Trial information is
+downloaded, converted and stored in a database.  Functions are included to
+identify deduplicated records, to easily find and extract variables (fields) of
+interest even from complex nesting as used by the registers, and to update
+previous queries.  The package can be used for meta-analysis and trend-analysis
+of the design and conduct as well as for results of clinical trials.")
+    (license license:expat)))
+
 (define-public r-ctrialsgov
   (package
     (name "r-ctrialsgov")
-- 
2.39.2

Message #22 received at 62441-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 62441-done <at> debbugs.gnu.org
Subject: Re: [bug#62441] [PATCH 1/4] gnu: Add r-ctrialsgov.
Date: Sun, 26 Mar 2023 19:01:42 +0200

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> writes:

> * gnu/packages/cran.scm (r-ctrialsgov): New variable.

We worked on the same patches at the same time.  I pushed this series
yesterday.  Thanks!

-- 
Ricardo

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