1. AnnotationForge
  2. NAMESPACE
Browse code

use https: rather than http: for NCBI access

- see https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge@121028 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 17/09/2016 05:57:07
Showing 1 changed files
NAMESPACE
History View file @ 31c6e71
... ... 
@@ -7,7 +7,7 @@ import(BiocGenerics)
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 import(S4Vectors)
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 import(AnnotationDbi)
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 import(XML)
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-
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+importFrom(RCurl, getURL)
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 exportClasses(
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     ## from R/AnnDbPkg-maker.R
Browse code

update ChipDb package templates to load DBI in unit tests

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge@118112 bc3139a8-67e5-0310-9ffc-ced21a209358

Valerie Obenchain authored on 02/06/2016 18:29:00
Showing 1 changed files
NAMESPACE
History View file @ a7457e4
... ... 
@@ -21,7 +21,7 @@ exportMethods(
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 export(
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     ## from R/AnnDbPkg-maker.R
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-    loadAnnDbPkgIndex,
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+    loadAnnDbPkgIndex, makeAnnDbPkg,
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     ## help functions for making sqlite files
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     populateDB,
Browse code

fix warnings related to ':::'

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge@116774 bc3139a8-67e5-0310-9ffc-ced21a209358

Valerie Obenchain authored on 25/04/2016 20:47:32
Showing 1 changed files
NAMESPACE
History View file @ 33d4718
... ... 
@@ -1,10 +1,13 @@
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-#import(methods)
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-#import(utils)
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+import(methods)
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+import(utils)
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 import(Biobase)
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 import(DBI)
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 import(RSQLite)
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 import(BiocGenerics)
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 import(S4Vectors)
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+import(AnnotationDbi)
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+import(XML)
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+
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 exportClasses(
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     ## from R/AnnDbPkg-maker.R
Browse code

Moves createSimpleBimap back where it belongs.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge@94798 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 01/10/2014 19:27:48
Showing 1 changed files
NAMESPACE
History View file @ 7107a70
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@@ -26,7 +26,6 @@ export(
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     ## wrapper functions for making chip packages
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     makeDBPackage,
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-    createSimpleBimap,
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     available.db0pkgs,
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     available.dbschemas,
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     available.chipdbschemas,
Browse code

need to import S4Vectors, at least for metadata()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge@89300 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 21/04/2014 18:20:36
Showing 1 changed files
NAMESPACE
History View file @ 2b7dde3
... ... 
@@ -4,7 +4,7 @@ import(Biobase)
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 import(DBI)
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 import(RSQLite)
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 import(BiocGenerics)
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-## importFrom(IRanges, metadata)
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+import(S4Vectors)
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 exportClasses(
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     ## from R/AnnDbPkg-maker.R
Browse code

Add source information to allow for building of new Inparanoid DBs.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge@87818 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 24/03/2014 22:37:21
Showing 1 changed files
NAMESPACE
History View file @ efd2de9
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@@ -44,6 +44,6 @@ export(
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     ## from R/makeProbePackage.R
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     getProbeDataAffy,
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     getProbeData_1lq,
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-    makeProbePackage
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-
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+    makeProbePackage,
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+    makeInpDb
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 )
Browse code

Adds skeleton for new function that aims to allow users to make chip packages more flexibly.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge@81712 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 15/10/2013 22:46:58
Showing 1 changed files
NAMESPACE
History View file @ a4273b7
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@@ -39,6 +39,7 @@ export(
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     ## This one will make you an org package from just data.frames:
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     makeOrgPackage,
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+    makeChipPackage,
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     ## from R/makeProbePackage.R
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     getProbeDataAffy,
Browse code

Finally exposes the makeOrgPackage() function that uses data.frames.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge@80425 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 14/09/2013 00:05:42
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NAMESPACE
History View file @ 488f57e
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@@ -36,7 +36,10 @@ export(
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     ## This one will make you an org package:
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     makeOrgPackageFromNCBI,
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-
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+
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+    ## This one will make you an org package from just data.frames:
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+    makeOrgPackage,
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+
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     ## from R/makeProbePackage.R
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     getProbeDataAffy,
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     getProbeData_1lq,
Browse code

Splits AnnoationDbi into AnnotationDbi and AnnotationForge

All the resources for creating annotations are getting bulky and need
to be put into another place. We are calling that place
AnnotationForge.


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge@66999 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 25/06/2012 18:39:17
Showing 1 changed files
NAMESPACE
History View file @ 8cc745f
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new file mode 100644
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@@ -0,0 +1,45 @@
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+#import(methods)
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+#import(utils)
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+import(Biobase)
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+import(DBI)
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+import(RSQLite)
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+import(BiocGenerics)
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+## importFrom(IRanges, metadata)
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+
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+exportClasses(
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+    ## from R/AnnDbPkg-maker.R
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+    "AnnDbPkgSeed"
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+
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+)
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+
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+exportMethods(
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+    "makeAnnDbPkg"
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+)
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+
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+export(
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+    ## from R/AnnDbPkg-maker.R
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+    loadAnnDbPkgIndex,
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+
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+    ## help functions for making sqlite files
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+    populateDB,
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+
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+    ## wrapper functions for making chip packages
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+    makeDBPackage,
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+
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+    createSimpleBimap,
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+    available.db0pkgs,
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+    available.dbschemas,
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+    available.chipdbschemas,
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+
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+    #Convenience function to make the intermediate DB pkgs
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+    wrapBaseDBPackages,
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+
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+    ## This one will make you an org package:
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+    makeOrgPackageFromNCBI,
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+
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+    ## from R/makeProbePackage.R
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+    getProbeDataAffy,
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+    getProbeData_1lq,
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+    makeProbePackage
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+
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+)