1. multiMiR
  2. DESCRIPTION
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:56:39
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DESCRIPTION
History View file @ 24d5ad4
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.22.0
5 
+Version: 1.23.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:56:39
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DESCRIPTION
History View file @ ba9546f
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.21.0
5 
+Version: 1.22.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:16:22
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DESCRIPTION
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.20.0
5 
+Version: 1.21.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:16:22
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DESCRIPTION
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.19.0
5 
+Version: 1.20.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:43:26
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DESCRIPTION
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.18.0
5 
+Version: 1.19.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:43:26
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DESCRIPTION
History View file @ 59a9d0c
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.17.0
5 
+Version: 1.18.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:38:12
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DESCRIPTION
History View file @ 74e644d
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.16.0
5 
+Version: 1.17.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:38:12
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DESCRIPTION
History View file @ 56f3190
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.15.0
5 
+Version: 1.16.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:30:26
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DESCRIPTION
History View file @ ce796ed
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.14.0
5 
+Version: 1.15.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:30:26
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DESCRIPTION
History View file @ 2166ba3
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.13.0
5 
+Version: 1.14.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 15:27:41
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DESCRIPTION
History View file @ 445f87b
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.12.0
5 
+Version: 1.13.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 15:27:41
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DESCRIPTION
History View file @ 21b8901
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.11.0
5 
+Version: 1.12.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 19:10:28
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DESCRIPTION
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.10.0
5 
+Version: 1.11.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 19:10:28
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DESCRIPTION
History View file @ 096b1cc
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.9.0
5 
+Version: 1.10.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:42:27
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DESCRIPTION
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.8.0
5 
+Version: 1.9.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:10:44
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DESCRIPTION
History View file @ 221900e
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.7.0
5 
+Version: 1.8.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:15:10
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DESCRIPTION
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.6.0
5 
+Version: 1.7.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:54:08
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DESCRIPTION
History View file @ c097006
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.5.0
5 
+Version: 1.6.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
Browse code

bioc handles version bumps I guess

Matt authored on 26/04/2019 06:02:55
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DESCRIPTION
History View file @ 97c5866
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.6.0
5 
+Version: 1.5.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
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updated matt's email

Matt authored on 26/04/2019 06:00:56
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DESCRIPTION
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@@ -5,7 +5,7 @@ Title:
5 5 
 Version: 1.6.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 
-      person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("cre", "aut")),
8 
+      person("Matt", "Mulvahill", email = "matt.mulvahill@gmail.com", role = c("cre", "aut")),
9 9 
       person("Spencer", "Mahaffey", email = "spencer.mahaffey@ucdenver.edu", role = c("aut")),
10 10 
       person("Katerina", "Kechris", email = "Katerina.Kechris@ucdenver.edu", role = c("aut", "cph", "ths")))
11 11 
 Description:
Browse code

Bioconductor says current version is 1.5 -- bumping from there to 1.6.0

Matt authored on 26/04/2019 05:50:38
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DESCRIPTION
History View file @ 2b3b62a
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.2.0
5 
+Version: 1.6.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("cre", "aut")),
Browse code

x.y.z version bump for new server url and new bioc release

Matt authored on 26/04/2019 05:45:20
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DESCRIPTION
History View file @ e3f49c7
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.1.0
5 
+Version: 1.2.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("cre", "aut")),
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:54:33
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DESCRIPTION
History View file @ 5b986e2
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 1.0.0
5 
+Version: 1.1.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("cre", "aut")),
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:41:52
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DESCRIPTION
History View file @ 841183b
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 0.99.7
5 
+Version: 1.0.0
6 6 
 Authors@R: c(
7 7 
       person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("cre", "aut")),
Browse code

resolving bioccheck errors.

Matt Mulvahill (MtEvans) authored on 03/10/2017 22:07:39
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DESCRIPTION
History View file @ a93a634
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@@ -3,9 +3,9 @@ Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 5 
 Version: 0.99.7
6 
-Authors@R:
7 
-    c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 
-      person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
6 
+Authors@R: c(
7 
+      person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 
+      person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("cre", "aut")),
9 9 
       person("Spencer", "Mahaffey", email = "spencer.mahaffey@ucdenver.edu", role = c("aut")),
10 10 
       person("Katerina", "Kechris", email = "Katerina.Kechris@ucdenver.edu", role = c("aut", "cph", "ths")))
11 11 
 Description:
... ... 
@@ -17,13 +17,13 @@ Description:
17 17 
 URL: https://github.com/KechrisLab/multiMiR
18 18 
 BugReports: https://github.com/KechrisLab/multiMiR/issues
19 19 
 Depends:
20 
-    R (>= 3.0)
20 
+    R (>= 3.4)
21 21 
 Imports:
22 
+    stats,
22 23 
     XML,
23 24 
     RCurl,
24 25 
     purrr (>= 0.2.2),
25 26 
     tibble (>= 1.2),
26 
-    magrittr,
27 27 
     methods,
28 28 
     BiocGenerics,
29 29 
     AnnotationDbi,
Browse code

partial change to returning single dataframe in @data slot instead of the 3 (validated/predicted/disease).

Matt Mulvahill (annapurna) authored on 03/10/2017 04:21:41
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DESCRIPTION
History View file @ 18c2c87
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@@ -25,7 +25,9 @@ Imports:
25 25 
     tibble (>= 1.2),
26 26 
     magrittr,
27 27 
     methods,
28 
-    AnnotationDbi
28 
+    BiocGenerics,
29 
+    AnnotationDbi,
30 
+    dplyr,
29 31 
 Suggests:
30 32 
     BiocStyle,
31 33 
     edgeR,
Browse code

version bump for bioconductoer submission.

Matt Mulvahill (annapurna) authored on 02/10/2017 16:31:30
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DESCRIPTION
History View file @ 8fc8eb8
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 0.99.6
5 
+Version: 0.99.7
6 6 
 Authors@R:
7 7 
     c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
Browse code

Dev branch is ready for Brian's new Bioc example. Merge branch 'exworkflow' into develop

Matt Mulvahill (MtEvans) authored on 29/09/2017 21:21:52
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Browse code

fixed bug in last commit -- removed dplyr import.

Matt Mulvahill (MtEvans) authored on 29/09/2017 07:32:47
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DESCRIPTION
History View file @ 0d651cf
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@@ -23,7 +23,6 @@ Imports:
23 23 
     RCurl,
24 24 
     purrr (>= 0.2.2),
25 25 
     tibble (>= 1.2),
26 
-    dplyr (>= 0.7.0),
27 26 
     magrittr,
28 27 
     methods,
29 28 
     AnnotationDbi
Browse code

added select -- bug with importFroms for generic AnnoDbi methods.

Matt Mulvahill (MtEvans) authored on 29/09/2017 07:28:25
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DESCRIPTION
History View file @ da9183f
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@@ -23,6 +23,7 @@ Imports:
23 23 
     RCurl,
24 24 
     purrr (>= 0.2.2),
25 25 
     tibble (>= 1.2),
26 
+    dplyr (>= 0.7.0),
26 27 
     magrittr,
27 28 
     methods,
28 29 
     AnnotationDbi
Browse code

working columns and keys methods -- documentation not right yet.

Matt Mulvahill (annapurna) authored on 28/09/2017 23:46:34
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DESCRIPTION
History View file @ 96eb1d3
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@@ -24,7 +24,8 @@ Imports:
24 24 
     purrr (>= 0.2.2),
25 25 
     tibble (>= 1.2),
26 26 
     magrittr,
27 
-    methods
27 
+    methods,
28 
+    AnnotationDbi
28 29 
 Suggests:
29 30 
     BiocStyle,
30 31 
     knitr,
Browse code

added s4 class for return object (mmquery_bioc), added legacy.out option to get_multimir, and cleaned up imports by using importFrom and removing namespace :: calls.

Matt Mulvahill (annapurna) authored on 28/09/2017 15:29:50
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DESCRIPTION
History View file @ 26fc098
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@@ -22,12 +22,14 @@ Imports:
22 22 
     XML,
23 23 
     RCurl,
24 24 
     purrr (>= 0.2.2),
25 
-    tibble (>= 1.2)
25 
+    tibble (>= 1.2),
26 
+    magrittr,
27 
+    methods
26 28 
 Suggests:
27 29 
     BiocStyle,
28 30 
     knitr,
29 31 
     rmarkdown,
30 
-    testthat (>= 1.0.2),
32 
+    testthat (>= 1.0.2)
31 33 
 VignetteBuilder: knitr
32 34 
 License: MIT + file LICENSE
33 35 
 LazyData: true
Browse code

added edgeR to Suggests and minor cleanup on example.

Matt Mulvahill (peregrine) authored on 27/09/2017 03:26:28
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DESCRIPTION
History View file @ 9836229
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@@ -25,6 +25,7 @@ Imports:
25 25 
     tibble (>= 1.2)
26 26 
 Suggests:
27 27 
     BiocStyle,
28 
+    edgeR,
28 29 
     knitr,
29 30 
     rmarkdown,
30 31 
     testthat (>= 1.0.2),
Browse code

moved tibble to imports from suggested in DESCRIPTION and imported specific functions used.

Matt Mulvahill (annapurna) authored on 20/09/2017 04:59:44
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DESCRIPTION
History View file @ 0e0e9c9
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@@ -21,13 +21,13 @@ Depends:
21 21 
 Imports:
22 22 
     XML,
23 23 
     RCurl,
24 
-    purrr (>= 0.2.2)
24 
+    purrr (>= 0.2.2),
25 
+    tibble (>= 1.2)
25 26 
 Suggests:
26 27 
     BiocStyle,
27 28 
     knitr,
28 29 
     rmarkdown,
29 30 
     testthat (>= 1.0.2),
30 
-    tibble (>= 1.2)
31 31 
 VignetteBuilder: knitr
32 32 
 License: MIT + file LICENSE
33 33 
 LazyData: true
Browse code

upping the version -- test if bioc issue will reopen.

Matt Mulvahill (annapurna) authored on 18/09/2017 17:39:50
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DESCRIPTION
History View file @ cb11e9d
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 0.99.5
5 
+Version: 0.99.6
6 6 
 Authors@R:
7 7 
     c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
Browse code

Lower required R version to 3.0 to match RCurl. See Issue #20.

Matt Mulvahill (peregrine) authored on 07/08/2017 15:26:35
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DESCRIPTION
History View file @ a2eec35
... ... 
@@ -17,7 +17,7 @@ Description:
17 17 
 URL: https://github.com/KechrisLab/multiMiR
18 18 
 BugReports: https://github.com/KechrisLab/multiMiR/issues
19 19 
 Depends:
20 
-    R (>= 3.4)
20 
+    R (>= 3.0)
21 21 
 Imports:
22 22 
     XML,
23 23 
     RCurl,
Browse code

Reverting sqltables changes in previous commit -- caused as-yet un-ID'd error in vignette example1 (2nd dataset queried).

Matt Mulvahill (annapurna) authored on 25/05/2017 19:51:05
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DESCRIPTION
History View file @ 6712962
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 0.99.4
5 
+Version: 0.99.5
6 6 
 Authors@R:
7 7 
     c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
Browse code

restructed some if/else logic to minimize times same logic is evaluated and to reduce line lengths. Still waiting on bioc-devel listserv confimration email.

Matt Mulvahill (annapurna) authored on 25/05/2017 18:13:19
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DESCRIPTION
History View file @ 9d4594d
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 0.99.3
5 
+Version: 0.99.4
6 6 
 Authors@R:
7 7 
     c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
Browse code

Version bump (v0.99.3) -- more bioc-devel warnings/errors resolved.

Matt Mulvahill (MtEvans) authored on 22/05/2017 23:16:19
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DESCRIPTION
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 0.99.2
5 
+Version: 0.99.3
6 6 
 Authors@R:
7 7 
     c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
Browse code

Rebuilt documentation --

Matt Mulvahill (MtEvans) authored on 22/05/2017 19:50:44
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DESCRIPTION
History View file @ 633711b
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 0.99.1
5 
+Version: 0.99.2
6 6 
 Authors@R:
7 7 
     c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
Browse code

Bumped to version 0.99.1 -- fixes made to resolve Bioc CHECK errors and attempt to retrigger build on Bioconductor submission.

Matt Mulvahill (MtEvans) authored on 22/05/2017 19:00:25
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DESCRIPTION
History View file @ 2219fc0
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 0.99.0
5 
+Version: 0.99.1
6 6 
 Authors@R:
7 7 
     c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
Browse code

added req'd version of purrr dependency.

Matt Mulvahill (MtEvans) authored on 22/05/2017 17:22:46
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DESCRIPTION
History View file @ 7dc6cc3
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@@ -21,7 +21,7 @@ Depends:
21 21 
 Imports:
22 22 
     XML,
23 23 
     RCurl,
24 
-    purrr
24 
+    purrr (>= 0.2.2)
25 25 
 Suggests:
26 26 
     BiocStyle,
27 27 
     knitr,
Browse code

bumped version (0.99.0) and required R version.

Matt Mulvahill (MtEvans) authored on 22/05/2017 17:14:07
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DESCRIPTION
History View file @ 947ef64
... ... 
@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 0.98.0.3
5 
+Version: 0.99.0
6 6 
 Authors@R:
7 7 
     c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
... ... 
@@ -17,7 +17,7 @@ Description:
17 17 
 URL: https://github.com/KechrisLab/multiMiR
18 18 
 BugReports: https://github.com/KechrisLab/multiMiR/issues
19 19 
 Depends:
20 
-    R (>= 3.3)
20 
+    R (>= 3.4)
21 21 
 Imports:
22 22 
     XML,
23 23 
     RCurl,
Browse code

removed one biocView on KK's request.

Matt Mulvahill (MtEvans) authored on 05/05/2017 20:46:38
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DESCRIPTION
History View file @ fc2584c
... ... 
@@ -32,7 +32,7 @@ VignetteBuilder: knitr
32 32 
 License: MIT + file LICENSE
33 33 
 LazyData: true
34 34 
 NeedsCompilation: no
35 
-biocViews: miRNAData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data,
36 
-    Rattus_norvegicus_Data, OrganismData
35 
+biocViews: miRNAData, Homo_sapiens_Data, Mus_musculus_Data,
36 
+    Rattus_norvegicus_Data, OrganismData
37 37 
 RoxygenNote: 6.0.1
38 38 
 Encoding: UTF-8
Browse code

corrected a few biocViews; added back osx to .travis.yml temporarily.

Matt Mulvahill (MtEvans) authored on 05/05/2017 19:47:49
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DESCRIPTION
History View file @ 6b741a6
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@@ -32,7 +32,7 @@ VignetteBuilder: knitr
32 32 
 License: MIT + file LICENSE
33 33 
 LazyData: true
34 34 
 NeedsCompilation: no
35 
-biocViews: miRNAData, SequencingData, Homo_sapiens_data, Mus_musculus_data,
36 
-    Rattus_norvegicus, OrganismData
35 
+biocViews: miRNAData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data,
36 
+    Rattus_norvegicus_Data, OrganismData
37 37 
 RoxygenNote: 6.0.1
38 38 
 Encoding: UTF-8
Browse code

Added biocViews (Bioconductor categories to add multiMiR to).

Matt Mulvahill (MtEvans) authored on 05/05/2017 19:29:33
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DESCRIPTION
History View file @ f101c47
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@@ -32,5 +32,7 @@ VignetteBuilder: knitr
32 32 
 License: MIT + file LICENSE
33 33 
 LazyData: true
34 34 
 NeedsCompilation: no
35 
+biocViews: miRNAData, SequencingData, Homo_sapiens_data, Mus_musculus_data,
36 
+    Rattus_norvegicus, OrganismData
35 37 
 RoxygenNote: 6.0.1
36 38 
 Encoding: UTF-8
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changed Spencer to an author from contributor.

Matt Mulvahill (annapurna) authored on 01/05/2017 20:20:58
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DESCRIPTION
History View file @ cdeee86
... ... 
@@ -2,11 +2,11 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 0.98.0.2
5 
+Version: 0.98.0.3
6 6 
 Authors@R:
7 7 
     c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
9 
-      person("Spencer", "Mahaffey", email = "spencer.mahaffey@ucdenver.edu", role = c("ctb")),
9 
+      person("Spencer", "Mahaffey", email = "spencer.mahaffey@ucdenver.edu", role = c("aut")),
10 10 
       person("Katerina", "Kechris", email = "Katerina.Kechris@ucdenver.edu", role = c("aut", "cph", "ths")))
11 11 
 Description:
12 12 
     A collection of microRNAs/targets from external resources, including
Browse code

incrementing version for beta testing on common version. includes about 8 commits of bug fixes, vignette updates.

Matt Mulvahill (peregrine) authored on 29/03/2017 21:32:53
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DESCRIPTION
History View file @ e16e3a6
... ... 
@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title:
3 3 
     Integration of multiple microRNA-target databases with their disease and
4 4 
     drug associations
5 
-Version: 0.98.0.1
5 
+Version: 0.98.0.2
6 6 
 Authors@R:
7 7 
     c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 8 
       person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
Browse code

added license, cleaned up descdription and added readme to buildignore.

Matt Mulvahill (annapurna) authored on 28/03/2017 20:18:24
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DESCRIPTION
History View file @ 33c3eda
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@@ -1,20 +1,36 @@
1 1 
 Package: multiMiR
2 
-Title: Integration of multiple microRNA-target databases with their
3 
-        disease and drug associations
4 
-Description: A collection of microRNAs/targets from external resources,
5 
-        including validated microRNA-target databases (miRecords, miRTarBase and
6 
-        TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm,
7 
-        miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases
8 
-        (miR2Disease, Pharmaco-miR VerSe and PhenomiR).
2 
+Title:
3 
+    Integration of multiple microRNA-target databases with their disease and
4 
+    drug associations
9 5 
 Version: 0.98.0.1
10 
-Author: Yuanbin Ru <ruyuanbin@gmail.com> and Katerina Kechris <Katerina.Kechris@ucdenver.edu>
11 
-Maintainer: Yuanbin Ru <ruyuanbin@gmail.com>
12 
-Depends: R (>= 3.3)
13 
-Imports: XML, RCurl, purrr
6 
+Authors@R:
7 
+    c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
8 
+      person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
9 
+      person("Spencer", "Mahaffey", email = "spencer.mahaffey@ucdenver.edu", role = c("ctb")),
10 
+      person("Katerina", "Kechris", email = "Katerina.Kechris@ucdenver.edu", role = c("aut", "cph", "ths")))
11 
+Description:
12 
+    A collection of microRNAs/targets from external resources, including
13 
+    validated microRNA-target databases (miRecords, miRTarBase and TarBase),
14 
+    predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm,
15 
+    miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug
16 
+    databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).
17 
+URL: https://github.com/KechrisLab/multiMiR
18 
+BugReports: https://github.com/KechrisLab/multiMiR/issues
19 
+Depends:
20 
+    R (>= 3.3)
21 
+Imports:
22 
+    XML,
23 
+    RCurl,
24 
+    purrr
25 
+Suggests:
26 
+    BiocStyle,
27 
+    knitr,
28 
+    rmarkdown,
29 
+    testthat (>= 1.0.2),
30 
+    tibble (>= 1.2)
14 31 
 VignetteBuilder: knitr
15 
-Suggests: BiocStyle, knitr, rmarkdown, testthat, tibble
16 
-License: file LICENSE
17 
-Packaged: 2016-12-08 04:19:34 UTC; smahaffey
32 
+License: MIT + file LICENSE
18 33 
 LazyData: true
19 34 
 NeedsCompilation: no
20 35 
 RoxygenNote: 6.0.1
36 
+Encoding: UTF-8
Browse code

removed multiMiR::: code used in testing, corrected documentation in sqlclauses and sqltables, added externallinks option into new code, moved 'summary' to own file and incroporated into new code, started print and summary methods for returned object, settled on final output object.

Matt Mulvahill (MtEvans) authored on 28/03/2017 04:07:26
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DESCRIPTION
History View file @ fe49926
... ... 
@@ -12,8 +12,7 @@ Maintainer: Yuanbin Ru <ruyuanbin@gmail.com>
12 12 
 Depends: R (>= 3.3)
13 13 
 Imports: XML, RCurl, purrr
14 14 
 VignetteBuilder: knitr
15 
-Suggests: BiocStyle, knitr, rmarkdown,
16 
-    testthat
15 
+Suggests: BiocStyle, knitr, rmarkdown, testthat, tibble
17 16 
 License: file LICENSE
18 17 
 Packaged: 2016-12-08 04:19:34 UTC; smahaffey
19 18 
 LazyData: true
Browse code

still making major changes. Added output object/constructor (still inprogress), added logic for invalid combos of options and tables, fixed some build errors (and likely added some new ones).

Matt Mulvahill (MtEvans) authored on 27/03/2017 07:35:40
Showing 1 changed files
DESCRIPTION
History View file @ 487d07e
... ... 
@@ -12,7 +12,8 @@ Maintainer: Yuanbin Ru <ruyuanbin@gmail.com>
12 12 
 Depends: R (>= 3.3)
13 13 
 Imports: XML, RCurl, purrr
14 14 
 VignetteBuilder: knitr
15 
-Suggests: BiocStyle, knitr, rmarkdown
15 
+Suggests: BiocStyle, knitr, rmarkdown,
16 
+    testthat
16 17 
 License: file LICENSE
17 18 
 Packaged: 2016-12-08 04:19:34 UTC; smahaffey
18 19 
 LazyData: true
Browse code

more progress on 'where' sql functions in dbclass

Matt Mulvahill (peregrine) authored on 23/03/2017 20:25:58
Showing 1 changed files
DESCRIPTION
History View file @ 7ac3074
... ... 
@@ -10,7 +10,7 @@ Version: 0.98.0.1
10 10 
 Author: Yuanbin Ru <ruyuanbin@gmail.com> and Katerina Kechris <Katerina.Kechris@ucdenver.edu>
11 11 
 Maintainer: Yuanbin Ru <ruyuanbin@gmail.com>
12 12 
 Depends: R (>= 3.3)
13 
-Imports: XML, RCurl
13 
+Imports: XML, RCurl, purrr
14 14 
 VignetteBuilder: knitr
15 15 
 Suggests: BiocStyle, knitr, rmarkdown
16 16 
 License: file LICENSE
Browse code

Note: Switched to Roxygen ~2 commits ago -- these are the files generated by devtools::document().

Matt Mulvahill (MtEvans) authored on 27/02/2017 06:23:38
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DESCRIPTION
History View file @ 6ba810f
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@@ -17,3 +17,4 @@ License: file LICENSE
17 17 
 Packaged: 2016-12-08 04:19:34 UTC; smahaffey
18 18 
 LazyData: true
19 19 
 NeedsCompilation: no
20 
+RoxygenNote: 6.0.1
Browse code

Rmd/html vignette in BiocStyle is working! Just need to test the time it takes to execute the code -- may be over the 6 (?) minute max. (Issue #11)

Matt Mulvahill (annapurna) authored on 03/01/2017 22:45:03
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DESCRIPTION
History View file @ 4755cda
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@@ -9,10 +9,10 @@ Description: A collection of microRNAs/targets from external resources,
9 9 
 Version: 0.98.0.1
10 10 
 Author: Yuanbin Ru <ruyuanbin@gmail.com> and Katerina Kechris <Katerina.Kechris@ucdenver.edu>
11 11 
 Maintainer: Yuanbin Ru <ruyuanbin@gmail.com>
12 
-Depends:
12 
+Depends: R (>= 3.3)
13 13 
 Imports: XML, RCurl
14 
-Suggests: BiocStyle, knitr, rmarkdown
15 14 
 VignetteBuilder: knitr
15 
+Suggests: BiocStyle, knitr, rmarkdown
16 16 
 License: file LICENSE
17 17 
 Packaged: 2016-12-08 04:19:34 UTC; smahaffey
18 18 
 LazyData: true
Browse code

more vignette fixes -- corrected inline code and added knitr options.

Matt Mulvahill (peregrine) authored on 03/01/2017 17:51:48
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DESCRIPTION
History View file @ bb2c827
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@@ -15,4 +15,5 @@ Suggests: BiocStyle, knitr, rmarkdown
15 15 
 VignetteBuilder: knitr
16 16 
 License: file LICENSE
17 17 
 Packaged: 2016-12-08 04:19:34 UTC; smahaffey
18 
+LazyData: true
18 19 
 NeedsCompilation: no
Browse code

finished converting, errors still occurring.

Matt Mulvahill (peregrine) authored on 14/12/2016 22:34:31
Showing 1 changed files
DESCRIPTION
History View file @ 13cbdc2
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@@ -11,7 +11,7 @@ Author: Yuanbin Ru <ruyuanbin@gmail.com> and Katerina Kechris <Katerina.Kechris@
11 11 
 Maintainer: Yuanbin Ru <ruyuanbin@gmail.com>
12 12 
 Depends:
13 13 
 Imports: XML, RCurl
14 
-Suggests: knitr, rmarkdown
14 
+Suggests: BiocStyle, knitr, rmarkdown
15 15 
 VignetteBuilder: knitr
16 16 
 License: file LICENSE
17 17 
 Packaged: 2016-12-08 04:19:34 UTC; smahaffey
Browse code

Changing vignetted to Rmd -- made it to about line 300. Check that code runs and use its output where possible (instead of verbatim blocks).

Matt Mulvahill (annapurna) authored on 14/12/2016 21:51:45
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DESCRIPTION
History View file @ e33d44b
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@@ -11,6 +11,8 @@ Author: Yuanbin Ru <ruyuanbin@gmail.com> and Katerina Kechris <Katerina.Kechris@
11 11 
 Maintainer: Yuanbin Ru <ruyuanbin@gmail.com>
12 12 
 Depends:
13 13 
 Imports: XML, RCurl
14 
+Suggests: knitr, rmarkdown
15 
+VignetteBuilder: knitr
14 16 
 License: file LICENSE
15 17 
 Packaged: 2016-12-08 04:19:34 UTC; smahaffey
16 18 
 NeedsCompilation: no
Browse code

Added and resolved changes in Spencer's v2.0.1.

Matt Mulvahill (peregrine) authored on 12/12/2016 07:37:57
Showing 1 changed files
DESCRIPTION
History View file @ a2ea779
... ... 
@@ -1,11 +1,16 @@
1 1 
 Package: multiMiR
2 2 
 Title: Integration of multiple microRNA-target databases with their
3 3 
         disease and drug associations
4 
-Description: A collection of microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).
5 
-Version: 0.98.0
4 
+Description: A collection of microRNAs/targets from external resources,
5 
+        including validated microRNA-target databases (miRecords, miRTarBase and
6 
+        TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm,
7 
+        miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases
8 
+        (miR2Disease, Pharmaco-miR VerSe and PhenomiR).
9 
+Version: 0.98.0.1
6 10 
 Author: Yuanbin Ru <ruyuanbin@gmail.com> and Katerina Kechris <Katerina.Kechris@ucdenver.edu>
7 11 
 Maintainer: Yuanbin Ru <ruyuanbin@gmail.com>
8 12 
 Depends:
9 13 
 Imports: XML, RCurl
10 14 
 License: file LICENSE
11 
-Packaged: 2015-05-20 21:55:51 UTC; yuanbin
15 
+Packaged: 2016-12-08 04:19:34 UTC; smahaffey
16 
+NeedsCompilation: no
Browse code

backed up revision to 0.98.0 -- saving 0.99.0 for first submission to Bioc.

Matt Mulvahill (peregrine) authored on 10/12/2016 18:34:17
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DESCRIPTION
History View file @ c7f0a07
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title: Integration of multiple microRNA-target databases with their
3 3 
         disease and drug associations
4 4 
 Description: A collection of microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).
5 
-Version: 0.99.0
5 
+Version: 0.98.0
6 6 
 Author: Yuanbin Ru <ruyuanbin@gmail.com> and Katerina Kechris <Katerina.Kechris@ucdenver.edu>
7 7 
 Maintainer: Yuanbin Ru <ruyuanbin@gmail.com>
8 8 
 Depends:
Browse code

updated versioning in prep for bioconductor. -- closes Issue #2.

Matt Mulvahill (peregrine) authored on 10/12/2016 07:54:55
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DESCRIPTION
History View file @ 0ac14fd
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@@ -2,7 +2,7 @@ Package: multiMiR
2 2 
 Title: Integration of multiple microRNA-target databases with their
3 3 
         disease and drug associations
4 4 
 Description: A collection of microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).
5 
-Version: 2.0
5 
+Version: 0.99.0
6 6 
 Author: Yuanbin Ru <ruyuanbin@gmail.com> and Katerina Kechris <Katerina.Kechris@ucdenver.edu>
7 7 
 Maintainer: Yuanbin Ru <ruyuanbin@gmail.com>
8 8 
 Depends:
Browse code

Initial commit. Version 2.0

Matt Mulvahill (peregrine) authored on 05/12/2016 05:30:28
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DESCRIPTION
History View file @ 1c0af51
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new file mode 100644
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@@ -0,0 +1,11 @@
1 
+Package: multiMiR
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+Title: Integration of multiple microRNA-target databases with their
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+        disease and drug associations
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+Description: A collection of microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).
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+Version: 2.0
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+Author: Yuanbin Ru <ruyuanbin@gmail.com> and Katerina Kechris <Katerina.Kechris@ucdenver.edu>
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+Maintainer: Yuanbin Ru <ruyuanbin@gmail.com>
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+Depends:
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+Imports: XML, RCurl
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+License: file LICENSE
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+Packaged: 2015-05-20 21:55:51 UTC; yuanbin