1. RGMQL
  2. DESCRIPTION
Browse code

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

J Wokaty authored on 01/11/2022 15:16:57
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DESCRIPTION
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1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.18.0
4 
+Version: 1.19.0
5 5 
 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
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            role = c("aut", "cre"),
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 15:16:57
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DESCRIPTION
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1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.17.0
4 
+Version: 1.18.0
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 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
7 7 
            role = c("aut", "cre"),
Browse code

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

Nitesh Turaga authored on 26/04/2022 15:46:12
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DESCRIPTION
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1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.16.0
4 
+Version: 1.17.0
5 5 
 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
7 7 
            role = c("aut", "cre"),
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bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:46:12
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DESCRIPTION
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1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.15.1
4 
+Version: 1.16.0
5 5 
 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
7 7 
            role = c("aut", "cre"),
Browse code

UnsupportedPlatforms mac

Sim1Pall8a authored on 18/11/2021 08:32:22
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DESCRIPTION
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1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.15.0
4 
+Version: 1.15.1
5 5 
 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
7 7 
            role = c("aut", "cre"),
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bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:40:49
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DESCRIPTION
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1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.14.0
4 
+Version: 1.15.0
5 5 
 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
7 7 
            role = c("aut", "cre"),
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 16:40:49
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.13.4
4 
+Version: 1.14.0
5 5 
 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
7 7 
            role = c("aut", "cre"),
Browse code

bump version

Simone authored on 19/07/2021 07:02:57
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.13.3
4 
+Version: 1.13.4
5 5 
 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
7 7 
            role = c("aut", "cre"),
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fixed error on gtf importing dataset files with seqid as other group columns

Simone authored on 17/07/2021 14:32:55
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.13.2
4 
+Version: 1.13.3
5 5 
 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
7 7 
            role = c("aut", "cre"),
Browse code

show_all_metadata use one rest call API

Simone authored on 26/05/2021 07:14:40
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.13.1
4 
+Version: 1.13.2
5 5 
 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
7 7 
            role = c("aut", "cre"),
Browse code

bump version .1

Simone authored on 25/05/2021 07:19:35
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DESCRIPTION
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1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.13.0
4 
+Version: 1.13.1
5 5 
 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
7 7 
            role = c("aut", "cre"),
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Squashed commit of the following: update version

Simone authored on 25/05/2021 07:07:31
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DESCRIPTION
History View file @ b65bdff
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old mode 100755
2 2 
new mode 100644
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.11.1
4 
+Version: 1.13.0
5 5 
 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
7 7 
            role = c("aut", "cre"),
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bump version

Simone authored on 17/05/2021 16:07:25
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.11.0
4 
+Version: 1.11.1
5 5 
 Authors@R: c(person(given = "Simone",
6 6 
            family = "Pallotta",
7 7 
            role = c("aut", "cre"),
Browse code

biocheck

Simone authored on 17/05/2021 09:41:45
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DESCRIPTION
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@@ -2,8 +2,15 @@ Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 4 
 Version: 1.11.0
5 
-Author: Simone Pallotta, Marco Masseroli
6 
-Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
5 
+Authors@R: c(person(given = "Simone",
6 
+           family = "Pallotta",
7 
+           role = c("aut", "cre"),
8 
+           email = "simonepallotta@hotmail.com"),
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+           person(given = "Marco",
10 
+           family = "Masseroli",
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+           role = "aut",
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+           email = "marco.masseroli@polimi.it")
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+           )
7 14 
 Description: This package brings the GenoMetric Query Language (GMQL)
8 15 
     functionalities into the R environment. GMQL is a high-level, declarative
9 16 
     language to manage heterogeneous genomic datasets for biomedical purposes,
Browse code

added logic to handle remote dataset, change name

Simone authored on 13/05/2021 14:35:27
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DESCRIPTION
History View file @ b15d477
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@@ -82,4 +82,5 @@ Collate:
82 82 
     'gmql_union.R'
83 83 
     'onLoad.R'
84 84 
     'ordering-functions.R'
85 
+    'show_all_metadata.R'
85 86 
     'web-services.R'
Browse code

Merge remote-tracking branch 'upstream/master'

Simone authored on 27/03/2021 15:30:59
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Browse code

add FULL() param to extract from GRangeslist

Simone authored on 27/03/2021 14:45:15
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DESCRIPTION
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@@ -61,8 +61,8 @@ Collate:
61 61 
     'S3Aggregates.R'
62 62 
     'S3Cover-Param.R'
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     'S3Distal.R'
64 
-    'S3filter_extract_param.R'
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     'S3Operator.R'
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+    'S3filter_extract_param.R'
66 66 
     'Utils.R'
67 67 
     'evaluation-functions.R'
68 68 
     'filter-extract-function.R'
Browse code

added FULL param to filter_extract function

Simone authored on 27/03/2021 14:32:41
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DESCRIPTION
History View file @ 7f0f9da
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@@ -61,6 +61,7 @@ Collate:
61 61 
     'S3Aggregates.R'
62 62 
     'S3Cover-Param.R'
63 63 
     'S3Distal.R'
64 
+    'S3filter_extract_param.R'
64 65 
     'S3Operator.R'
65 66 
     'Utils.R'
66 67 
     'evaluation-functions.R'
Browse code

update with some news

Simone authored on 21/03/2021 14:34:30
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DESCRIPTION
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old mode 100644
2 2 
new mode 100755
Browse code

fix take and read

Simone authored on 09/02/2021 09:07:32
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DESCRIPTION
History View file @ 4ad2435
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@@ -23,7 +23,7 @@ License: Artistic-2.0
23 23 
 URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/
24 24 
 Encoding: UTF-8
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 LazyData: true
26 
-RoxygenNote: 6.1.1
26 
+RoxygenNote: 7.1.1
27 27 
 Imports:
28 28 
     httr,
29 29 
     rJava,
Browse code

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

Nitesh Turaga authored on 27/10/2020 15:31:01
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.10.0
4 
+Version: 1.11.0
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
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 15:31:01
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.9.3
4 
+Version: 1.10.0
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

update vignette with windows issue, bump version

Simone authored on 27/10/2020 10:06:13
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.9.2
4 
+Version: 1.9.3
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

unsupported on 32-bit Windows (no more JDK for 32-bit Windows)

Hervé Pagès authored on 01/09/2020 19:52:16
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.9.1
4 
+Version: 1.9.2
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

The GMQLDataset class does not need to extend DataTable

Virtual class DataTable will be removed from the S4Vectors package
in the near future.

Hervé Pagès authored on 02/05/2020 09:03:41
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.9.0
4 
+Version: 1.9.1
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

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

Nitesh Turaga authored on 27/04/2020 19:12:55
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DESCRIPTION
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1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.8.0
4 
+Version: 1.9.0
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
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 19:12:55
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DESCRIPTION
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1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.7.0
4 
+Version: 1.8.0
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

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

Nitesh Turaga authored on 29/10/2019 17:42:38
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DESCRIPTION
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1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.6.0
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+Version: 1.7.0
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
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 17:10:56
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DESCRIPTION
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1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.5.1
4 
+Version: 1.6.0
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

minor fix

Simone authored on 09/06/2019 11:05:22
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DESCRIPTION
History View file @ e8be679
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@@ -23,7 +23,7 @@ License: Artistic-2.0
23 23 
 URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/
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 Encoding: UTF-8
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 LazyData: true
26 
-RoxygenNote: 6.1.0
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+RoxygenNote: 6.1.1
27 27 
 Imports:
28 28 
     httr,
29 29 
     rJava,
Browse code

new version

Simone authored on 06/05/2019 19:08:27
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.5.0
4 
+Version: 1.5.1
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

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

Nitesh Turaga authored on 02/05/2019 16:15:33
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.4.0
4 
+Version: 1.5.0
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
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 15:54:10
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DESCRIPTION
History View file @ fa8a934
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.3.0
4 
+Version: 1.4.0
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

change description and sync

Simone authored on 07/12/2018 11:13:51
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DESCRIPTION
History View file @ 0caa376
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@@ -51,6 +51,7 @@ biocViews:
51 51 
     Infrastructure,
52 52 
     DataImport,
53 53 
     Network,
54 
+    ImmunoOncology,
54 55 
     SingleCell
55 56 
 Collate:
56 57 
     'AllClasses.R'
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:38
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.2.0
4 
+Version: 1.3.0
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:42:07
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DESCRIPTION
History View file @ 59df469
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
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-Version: 1.1.0
4 
+Version: 1.2.0
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

Fixed conflicts in version change

Simone authored on 18/09/2018 16:00:05
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DESCRIPTION
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@@ -1,11 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
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-<<<<<<< HEAD
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-Version: 1.0.1
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-=======
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 Version: 1.1.0
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->>>>>>> upstream/master
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 Author: Simone Pallotta, Marco Masseroli
10 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
11 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

fixed url

Simone authored on 23/08/2018 06:43:54
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Browse code

fixed url

Simone authored on 16/08/2018 09:03:55
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DESCRIPTION
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1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
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-Version: 0.99.12
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+Version: 1.0.1
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
... ... 
@@ -23,7 +23,7 @@ License: Artistic-2.0
23 23 
 URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/
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 Encoding: UTF-8
25 25 
 LazyData: true
26 
-RoxygenNote: 6.0.1
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+RoxygenNote: 6.1.0
27 27 
 Imports:
28 28 
     httr,
29 29 
     rJava,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:43
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 1.0.0
4 
+Version: 1.1.0
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:49
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
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-Version: 0.99.12
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+Version: 1.0.0
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

fixed export GTF

Simone authored on 28/04/2018 08:44:07
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DESCRIPTION
History View file @ ac43eae
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.11
4 
+Version: 0.99.12
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

new build

Simone authored on 21/04/2018 16:56:40
Showing 1 changed files
DESCRIPTION
History View file @ bbd7f21
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.10
4 
+Version: 0.99.11
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

new build

Simone authored on 20/04/2018 18:40:27
Showing 1 changed files
DESCRIPTION
History View file @ 24fedfb
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.9
4 
+Version: 0.99.10
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

new version

Simone authored on 28/02/2018 17:29:58
Showing 1 changed files
DESCRIPTION
History View file @ eb75845
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.44
4 
+Version: 0.99.9
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

fix join and serialize

Simone authored on 29/01/2018 10:19:59
Showing 1 changed files
DESCRIPTION
History View file @ 2b8c564
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.43
4 
+Version: 0.99.44
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

new version

Simone authored on 21/01/2018 10:30:12
Showing 1 changed files
DESCRIPTION
History View file @ da55d3c
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.42
4 
+Version: 0.99.43
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

minor fix

Simone authored on 11/01/2018 13:10:15
Showing 1 changed files
DESCRIPTION
History View file @ 1869707
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.41
4 
+Version: 0.99.42
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
... ... 
@@ -11,7 +11,7 @@ Description: This package brings the GenoMetric Query Language (GMQL)
11 11 
 	GMQL adopts algorithms efficiently designed for big data using cloud-computing
12 12 
     technologies (like Apache Hadoop and Spark) allowing GMQL to run on modern
13 13 
 	infrastructures, in order to achieve scalability and high performance.
14 
-	It allows to to create, manipulate and extract genomic data from different
14 
+	It allows to create, manipulate and extract genomic data from different
15 15 
 	data sources both locally and remotely. Our RGMQL functions allow complex
16 16 
 	queries and processing leveraging on the R idiomatic paradigm.
17 17 
 	The RGMQL package also provides a rich set of ancillary classes that allow
Browse code

minor fix

Simone authored on 08/01/2018 12:44:14
Showing 1 changed files
DESCRIPTION
History View file @ 2e3261f
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.40
4 
+Version: 0.99.41
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

minor fix

Simone authored on 05/01/2018 08:31:03
Showing 1 changed files
DESCRIPTION
History View file @ 099f11d
... ... 
@@ -1,48 +1,24 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.38
4 
+Version: 0.99.40
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
8 8 
     functionalities into the R environment. GMQL is a high-level, declarative
9 
-    language to query and compare multiple and heterogeneous genomic datasets
10 
-    for biomedical knowledge discovery. It allows expressing easily queries and
11 
-    processing over genomic regions and their metadata, to extract genomic regions
12 
-    of interest and compute their properties. GMQL adopts algorithms designed
13 
-    for big data and their efficient implementation using cloud-computing
14 
-    technologies, including Apache Hadoop framework and Spark engine;
15 
-    these make GMQL able to run on modern high performance computing
16 
-    infrastructures, CPU clusters and network infrastructures, in order to achieve
17 
-    scalability and performance on big data. This RGMQL package is built over
18 
-    a scalable data management engine written in Scala programming language,
19 
-    released as Scala API; it provides a set of functions to create,
20 
-    manipulate and extract genomic data from different data sources both
21 
-    from local and remote datasets. These RGMQL functions allow performing
22 
-    complex queries and processing without knowing the GMQL syntax,
23 
-    but leveraging on R idiomatic paradigm and logic. RGMQL provides two different
24 
-    approaches in writing GMQL queries and processing scripts: a) REST calls b)
25 
-    standard R APIs The REST approach let users to log into a remote infrastructure
26 
-    where a GMQL system is installed, and manage remote big genomic datasets hosted
27 
-    in cluster-based repository. User can download an entire remote dataset into
28 
-    local folder, upload local datasets into the remote repository or compiling
29 
-    and running a textual query or processing script just invoking the right RGMQL
30 
-    functions. Multiple REST invocations can be invoked and run concurrently on
31 
-    remote infrastructure allowing user to monitor the progress status of every
32 
-    call. Many other REST functionalities are available in order to allow a complete
33 
-    interaction with remote infrastructure. The R APIs approach lets user work with
34 
-    local or remote datasets using batch-like style where single invocations must
35 
-    be invoked sequentially; with this approach all GMQL queries and processing
36 
-    can be written as a sequence of RGMQL functions. Unlike other similar packages,
37 
-    every RGMQL function simply builds a query, with no intermediate result shown
38 
-    (except for a few functions that execute queries and for some utility functions
39 
-    for interoperability with other packages) The RGMQL package also provides a rich
40 
-    set of ancillary classes that allow sophisticated input/output management and
41 
-    sorting, such as ASC, DESC, BAG, MIN, MAX, SUM, AVG, MEDIAN, STD, Q1, Q2, Q3,
42 
-    and several others; these classes are used only to build predicates and complex
43 
-    conditions taken as input by RGMQL functions; Note that many RGMQL functions are
44 
-    not directly executed in R environment, but are deferred until real execution is
45 
-    issued.
9 
+    language to manage heterogeneous genomic datasets for biomedical purposes,
10 
+	using simple queries to process genomic regions and their metadata and properties.
11 
+	GMQL adopts algorithms efficiently designed for big data using cloud-computing
12 
+    technologies (like Apache Hadoop and Spark) allowing GMQL to run on modern
13 
+	infrastructures, in order to achieve scalability and high performance.
14 
+	It allows to to create, manipulate and extract genomic data from different
15 
+	data sources both locally and remotely. Our RGMQL functions allow complex
16 
+	queries and processing leveraging on the R idiomatic paradigm.
17 
+	The RGMQL package also provides a rich set of ancillary classes that allow
18 
+	sophisticated input/output management and sorting, such as:
19 
+	ASC, DESC, BAG, MIN, MAX, SUM, AVG, MEDIAN, STD, Q1, Q2, Q3 (and many others).
20 
+	Note that many RGMQL functions are not directly executed in R environment,
21 
+	but are deferred until real execution is issued.
46 22 
 License: Artistic-2.0
47 23 
 URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/
48 24 
 Encoding: UTF-8
... ... 
@@ -64,7 +40,7 @@ Imports:
64 40 
     glue,
65 41 
     BiocGenerics
66 42 
 Depends:
67 
-    R(<= 3.4.2), RGMQLlib
43 
+    R(>= 3.4.2), RGMQLlib
68 44 
 VignetteBuilder: knitr
69 45 
 Suggests:
70 46 
     BiocStyle,
Browse code

check fix

Simone authored on 03/01/2018 11:26:05
Showing 1 changed files
DESCRIPTION
History View file @ 2f53c9a
... ... 
@@ -64,7 +64,7 @@ Imports:
64 64 
     glue,
65 65 
     BiocGenerics
66 66 
 Depends:
67 
-    R(<= 3.4.2), RGMQLScalaLib
67 
+    R(<= 3.4.2), RGMQLlib
68 68 
 VignetteBuilder: knitr
69 69 
 Suggests:
70 70 
     BiocStyle,
Browse code

change description

Simone authored on 02/01/2018 09:53:44
Showing 1 changed files
DESCRIPTION
History View file @ bcce6e7
... ... 
@@ -64,7 +64,7 @@ Imports:
64 64 
     glue,
65 65 
     BiocGenerics
66 66 
 Depends:
67 
-    R(<= 3.4.2), RGMQLScalaLibs
67 
+    R(<= 3.4.2), RGMQLScalaLib
68 68 
 VignetteBuilder: knitr
69 69 
 Suggests:
70 70 
     BiocStyle,
Browse code

delete jar

Simone authored on 01/01/2018 13:44:59
Showing 1 changed files
DESCRIPTION
History View file @ 40ec852
... ... 
@@ -8,21 +8,18 @@ Description: This package brings the GenoMetric Query Language (GMQL)
8 8 
     functionalities into the R environment. GMQL is a high-level, declarative
9 9 
     language to query and compare multiple and heterogeneous genomic datasets
10 10 
     for biomedical knowledge discovery. It allows expressing easily queries and
11 
-    processing over genomic regions and their metadata, in a way similar to what
12 
-    can be done with the Structured Query Language (SQL) over a relational database,
13 
-    to extract genomic regions of interest and compute their properties. GMQL
14 
-    adopts algorithms designed for big data and their efficient implementation
15 
-    using cloud-computing technologies, including Apache Hadoop framework and
16 
-    Spark engine; these make GMQL able to run on modern high performance computing
11 
+    processing over genomic regions and their metadata, to extract genomic regions
12 
+    of interest and compute their properties. GMQL adopts algorithms designed
13 
+    for big data and their efficient implementation using cloud-computing
14 
+    technologies, including Apache Hadoop framework and Spark engine;
15 
+    these make GMQL able to run on modern high performance computing
17 16 
     infrastructures, CPU clusters and network infrastructures, in order to achieve
18 
-    scalability and performance on big data. With GMQL very complex genomic
19 
-    operations can be written as simple queries, with implicit iteration over
20 
-    thousands of heterogeneous samples, and computed efficiently in few minutes over
21 
-    servers or clouds. This RGMQL package is built over a scalable data management
22 
-    engine written in Scala programming language, released as Scala API; it provides
23 
-    a set of functions to create, manipulate and extract genomic data from different
24 
-    data sources both from local and remote datasets. These RGMQL functions allow
25 
-    performing complex queries and processing without knowing the GMQL syntax,
17 
+    scalability and performance on big data. This RGMQL package is built over
18 
+    a scalable data management engine written in Scala programming language,
19 
+    released as Scala API; it provides a set of functions to create,
20 
+    manipulate and extract genomic data from different data sources both
21 
+    from local and remote datasets. These RGMQL functions allow performing
22 
+    complex queries and processing without knowing the GMQL syntax,
26 23 
     but leveraging on R idiomatic paradigm and logic. RGMQL provides two different
27 24 
     approaches in writing GMQL queries and processing scripts: a) REST calls b)
28 25 
     standard R APIs The REST approach let users to log into a remote infrastructure
... ... 
@@ -67,7 +64,7 @@ Imports:
67 64 
     glue,
68 65 
     BiocGenerics
69 66 
 Depends:
70 
-    R(>= 3.4.2)
67 
+    R(<= 3.4.2), RGMQLScalaLibs
71 68 
 VignetteBuilder: knitr
72 69 
 Suggests:
73 70 
     BiocStyle,
Browse code

fix

Simone authored on 10/12/2017 16:29:05
Showing 1 changed files
DESCRIPTION
History View file @ 83eb062
... ... 
@@ -95,6 +95,7 @@ Collate:
95 95 
     'gmql_difference.R'
96 96 
     'gmql_extend.R'
97 97 
     'gmql_group.R'
98 
+    'gmql_init.R'
98 99 
     'gmql_join.R'
99 100 
     'gmql_map.R'
100 101 
     'gmql_materialize.R'
Browse code

start new build

Simone authored on 06/12/2017 17:51:02
Showing 1 changed files
DESCRIPTION
History View file @ a1b1ec0
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.37
4 
+Version: 0.99.38
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
... ... 
@@ -67,7 +67,7 @@ Imports:
67 67 
     glue,
68 68 
     BiocGenerics
69 69 
 Depends:
70 
-    R(<= 3.4.2)
70 
+    R(>= 3.4.2)
71 71 
 VignetteBuilder: knitr
72 72 
 Suggests:
73 73 
     BiocStyle,
Browse code

fix and clean

Simone authored on 06/12/2017 17:47:26
Showing 1 changed files
DESCRIPTION
History View file @ e5131ba
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.36
4 
+Version: 0.99.37
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
... ... 
@@ -82,7 +82,6 @@ biocViews:
82 82 
 Collate:
83 83 
     'AllClasses.R'
84 84 
     'AllGenerics.R'
85 
-    'GMQL4TFarm.R'
86 85 
     'GMQLtoGRanges.R'
87 86 
     'GRangesToGMQL.R'
88 87 
     'S3Aggregates.R'
... ... 
@@ -91,6 +90,7 @@ Collate:
91 90 
     'S3Operator.R'
92 91 
     'Utils.R'
93 92 
     'evaluation-functions.R'
93 
+    'filter-extract-function.R'
94 94 
     'gmql_cover.R'
95 95 
     'gmql_difference.R'
96 96 
     'gmql_extend.R'
Browse code

add group, fixed some function

Simone authored on 05/12/2017 10:34:47
Showing 1 changed files
DESCRIPTION
History View file @ c760228
... ... 
@@ -63,7 +63,9 @@ Imports:
63 63 
     methods,
64 64 
     S4Vectors,
65 65 
     dplyr,
66 
-    stats
66 
+    stats,
67 
+    glue,
68 
+    BiocGenerics
67 69 
 Depends:
68 70 
     R(<= 3.4.2)
69 71 
 VignetteBuilder: knitr
... ... 
@@ -92,6 +94,7 @@ Collate:
92 94 
     'gmql_cover.R'
93 95 
     'gmql_difference.R'
94 96 
     'gmql_extend.R'
97 
+    'gmql_group.R'
95 98 
     'gmql_join.R'
96 99 
     'gmql_map.R'
97 100 
     'gmql_materialize.R'
Browse code

fix join

Simone authored on 24/11/2017 20:25:53
Showing 1 changed files
DESCRIPTION
History View file @ 971c90b
... ... 
@@ -65,7 +65,7 @@ Imports:
65 65 
     dplyr,
66 66 
     stats
67 67 
 Depends:
68 
-    R(>= 3.4.2)
68 
+    R(<= 3.4.2)
69 69 
 VignetteBuilder: knitr
70 70 
 Suggests:
71 71 
     BiocStyle,
Browse code

clean files and folder

Simone authored on 21/11/2017 13:43:55
Showing 1 changed files
DESCRIPTION
History View file @ 48ab60c
... ... 
@@ -78,31 +78,29 @@ biocViews:
78 78 
     Network,
79 79 
     SingleCell
80 80 
 Collate:
81 
-    'GMQLDataset-class.R'
82 
-    'Cover.R'
83 
-    'Difference.R'
84 
-    'Extend.R'
81 
+    'AllClasses.R'
82 
+    'AllGenerics.R'
85 83 
     'GMQL4TFarm.R'
86 84 
     'GMQLtoGRanges.R'
87 85 
     'GRangesToGMQL.R'
88 
-    'Join.R'
89 
-    'Map.R'
90 
-    'Materialize.R'
91 
-    'Merge.R'
92 
-    'Order.R'
93 
-    'Project.R'
94 
-    'Read.R'
95 
-    'Select.R'
96 
-    'Union.R'
86 
+    'S3Aggregates.R'
87 
+    'S3Cover-Param.R'
88 
+    'S3Distal.R'
89 
+    'S3Operator.R'
97 90 
     'Utils.R'
98 
-    'aggregate-class.R'
99 
-    'authOp.R'
100 
-    'browseOp.R'
101 
-    'cover_param-class.R'
102 
-    'datasetOp.R'
103 
-    'distal-class.R'
104 
-    'evaluation_functions.R'
91 
+    'evaluation-functions.R'
92 
+    'gmql_cover.R'
93 
+    'gmql_difference.R'
94 
+    'gmql_extend.R'
95 
+    'gmql_join.R'
96 
+    'gmql_map.R'
97 
+    'gmql_materialize.R'
98 
+    'gmql_merge.R'
99 
+    'gmql_order.R'
100 
+    'gmql_project.R'
101 
+    'gmql_read.R'
102 
+    'gmql_select.R'
103 
+    'gmql_union.R'
105 104 
     'onLoad.R'
106 
-    'operator-class.R'
107 
-    'ordering-class.R'
108 
-    'queryOp.R'
105 
+    'ordering-functions.R'
106 
+    'web-services.R'
Browse code

new build

Simone authored on 19/11/2017 00:55:40
Showing 1 changed files
DESCRIPTION
History View file @ 86c398f
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.35
4 
+Version: 0.99.36
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

new build

Simone authored on 17/11/2017 14:46:01
Showing 1 changed files
DESCRIPTION
History View file @ 7f5ebc0
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.34
4 
+Version: 0.99.35
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
Browse code

S4 methods and change help

Simone authored on 17/11/2017 14:45:18
Showing 1 changed files
DESCRIPTION
History View file @ 65260a4
... ... 
@@ -98,10 +98,10 @@ Collate:
98 98 
     'aggregate-class.R'
99 99 
     'authOp.R'
100 100 
     'browseOp.R'
101 
-    'condition-class.R'
102 101 
     'cover_param-class.R'
103 102 
     'datasetOp.R'
104 103 
     'distal-class.R'
104 
+    'evaluation_functions.R'
105 105 
     'onLoad.R'
106 106 
     'operator-class.R'
107 107 
     'ordering-class.R'
Browse code

start new build

Simone authored on 16/11/2017 12:08:21
Showing 1 changed files
DESCRIPTION
History View file @ 702b843
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.32
4 
+Version: 0.99.34
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings the GenoMetric Query Language (GMQL)
... ... 
@@ -63,8 +63,7 @@ Imports:
63 63 
     methods,
64 64 
     S4Vectors,
65 65 
     dplyr,
66 
-    stats,
67 
-    BiocGenerics
66 
+    stats
68 67 
 Depends:
69 68 
     R(>= 3.4.2)
70 69 
 VignetteBuilder: knitr
Browse code

map to s4 - start new build

Simone authored on 16/11/2017 10:37:54
Showing 1 changed files
DESCRIPTION
History View file @ b3e9c8a
... ... 
@@ -1,10 +1,10 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.31
4 
+Version: 0.99.32
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 
-Description: This RGMQL package brings the GenoMetric Query Language (GMQL)
7 
+Description: This package brings the GenoMetric Query Language (GMQL)
8 8 
     functionalities into the R environment. GMQL is a high-level, declarative
9 9 
     language to query and compare multiple and heterogeneous genomic datasets
10 10 
     for biomedical knowledge discovery. It allows expressing easily queries and
... ... 
@@ -63,12 +63,47 @@ Imports:
63 63 
     methods,
64 64 
     S4Vectors,
65 65 
     dplyr,
66 
-    stats
66 
+    stats,
67 
+    BiocGenerics
67 68 
 Depends:
68 69 
     R(>= 3.4.2)
69 70 
 VignetteBuilder: knitr
70 
-Suggests:
71 
+Suggests:
71 72 
     BiocStyle,
72 73 
     knitr,
73 74 
     rmarkdown
74 
-biocViews: Software,Infrastructure,DataImport,Network,SingleCell
75 
+biocViews:
76 
+    Software,
77 
+    Infrastructure,
78 
+    DataImport,
79 
+    Network,
80 
+    SingleCell
81 
+Collate:
82 
+    'GMQLDataset-class.R'
83 
+    'Cover.R'
84 
+    'Difference.R'
85 
+    'Extend.R'
86 
+    'GMQL4TFarm.R'
87 
+    'GMQLtoGRanges.R'
88 
+    'GRangesToGMQL.R'
89 
+    'Join.R'
90 
+    'Map.R'
91 
+    'Materialize.R'
92 
+    'Merge.R'
93 
+    'Order.R'
94 
+    'Project.R'
95 
+    'Read.R'
96 
+    'Select.R'
97 
+    'Union.R'
98 
+    'Utils.R'
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+    'aggregate-class.R'
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+    'authOp.R'
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+    'browseOp.R'
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+    'condition-class.R'
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+    'cover_param-class.R'
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+    'datasetOp.R'
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+    'distal-class.R'
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+    'onLoad.R'
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+    'operator-class.R'
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+    'ordering-class.R'
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+    'queryOp.R'
Browse code

start new build

Simone authored on 15/11/2017 07:36:20
Showing 1 changed files
DESCRIPTION
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@@ -1,7 +1,7 @@
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 Package: RGMQL
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 Type: Package
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 Title: GenoMetric Query Language for R/Bioconductor
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-Version: 0.99.30
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+Version: 0.99.31
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 Author: Simone Pallotta, Marco Masseroli
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 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
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 Description: This RGMQL package brings the GenoMetric Query Language (GMQL)
Browse code

start new build

Simone authored on 14/11/2017 17:42:59
Showing 1 changed files
DESCRIPTION
History View file @ 68a0f34
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@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
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-Version: 0.99.29
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+Version: 0.99.30
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 Author: Simone Pallotta, Marco Masseroli
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 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
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 Description: This RGMQL package brings the GenoMetric Query Language (GMQL)
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@@ -53,7 +53,8 @@ LazyData: true
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 RoxygenNote: 6.0.1
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 Imports:
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     httr,
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-    rJava,GenomicRanges,
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