[med-svn] [r-bioc-annotationhub] 01/04: New upstream version 2.8.3
Andreas Tille
tille at debian.org
Thu Nov 9 09:09:18 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-annotationhub.
commit fbb6aadfed995c58393efa8fd9887276544d66e7
Author: Andreas Tille <tille at debian.org>
Date: Thu Oct 19 21:47:43 2017 +0200
New upstream version 2.8.3
---
DESCRIPTION | 4 +--
R/sql-utils.R | 1 +
build/vignette.rds | Bin 287 -> 287 bytes
inst/doc/AnnotationHub-HOWTO.html | 54 +++++++++++++++----------------
inst/doc/AnnotationHub.html | 65 ++++++++++++++++++++------------------
5 files changed, 64 insertions(+), 60 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index a24bbfd..9a1be67 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: AnnotationHub
Type: Package
Title: Client to access AnnotationHub resources
-Version: 2.8.2
+Version: 2.8.3
Authors at R:
c(person("Martin", "Morgan", email="martin.morgan at roswellpark.org",
role="cre"),
@@ -40,4 +40,4 @@ Author: Martin Morgan [cre],
Marc Carlson [ctb],
Dan Tenenbaum [ctb],
Sonali Arora [ctb]
-Packaged: 2017-06-10 23:23:37 UTC; biocbuild
+Packaged: 2017-10-17 23:20:03 UTC; biocbuild
diff --git a/R/sql-utils.R b/R/sql-utils.R
index 31631ff..e007e17 100644
--- a/R/sql-utils.R
+++ b/R/sql-utils.R
@@ -87,6 +87,7 @@
FROM resources, biocversions, rdatapaths
WHERE biocversions.biocversion == "%s"
AND rdatapaths.rdataclass == "OrgDb"
+ AND resources.rdatadateremoved IS NULL
AND biocversions.resource_id == resources.id
AND rdatapaths.resource_id == resources.id',
orgdb_release_version)
diff --git a/build/vignette.rds b/build/vignette.rds
index e48a15b..6e1b8bc 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/AnnotationHub-HOWTO.html b/inst/doc/AnnotationHub-HOWTO.html
index 1076cdd..32e2589 100644
--- a/inst/doc/AnnotationHub-HOWTO.html
+++ b/inst/doc/AnnotationHub-HOWTO.html
@@ -77,7 +77,7 @@ document.addEventListener("DOMContentLoaded", function() {
links[i].target = '_blank';
});
</script>
-<p><strong>Package</strong>: <em><a href="http://bioconductor.org/packages/AnnotationHub">AnnotationHub</a></em><br /> <strong>Authors</strong>: Martin Morgan [cre], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb]<br /> <strong>Modified</strong>: Sun Jun 28 10:41:23 2015<br /> <strong>Compiled</strong>: Sat Jun 10 19:22:37 2017</p>
+<p><strong>Package</strong>: <em><a href="http://bioconductor.org/packages/AnnotationHub">AnnotationHub</a></em><br /> <strong>Authors</strong>: Martin Morgan [cre], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb]<br /> <strong>Modified</strong>: Sun Jun 28 10:41:23 2015<br /> <strong>Compiled</strong>: Tue Oct 17 19:18:58 2017</p>
<div id="accessing-genome-scale-data" class="section level1">
<h1><span class="header-section-number">1</span> Accessing Genome-Scale Data</h1>
<div id="non-model-organism-gene-annotations" class="section level2">
@@ -447,8 +447,6 @@ chainfiles</code></pre>
<p>Perform the liftOver operation using <code>rtracklayer::liftOver()</code>:</p>
<pre class="r"><code>library(rtracklayer)
gr38 <- liftOver(peaks, chain)</code></pre>
-<pre><code>## Warning: closing unused connection 6 (/tmp/Rtmprm2Zka/file28c86026b3d3)</code></pre>
-<pre><code>## Warning: closing unused connection 5 (/tmp/Rtmprm2Zka/file28c84dffa6ed)</code></pre>
<p>This returns a <em>GRangeslist</em>; update the genome of the result to get the final result</p>
<pre class="r"><code>genome(gr38) <- "hg38"
gr38</code></pre>
@@ -663,9 +661,9 @@ overlap[idx]</code></pre>
<div id="sessioninfo" class="section level1">
<h1><span class="header-section-number">2</span> sessionInfo</h1>
<pre class="r"><code>sessionInfo()</code></pre>
-<pre><code>## R version 3.4.0 (2017-04-21)
+<pre><code>## R version 3.4.2 (2017-09-28)
## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Ubuntu 16.04.2 LTS
+## Running under: Ubuntu 16.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.5-bioc/R/lib/libRblas.so
@@ -681,31 +679,33 @@ overlap[idx]</code></pre>
## [1] stats4 parallel stats graphics grDevices utils datasets methods base
##
## other attached packages:
-## [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.44.0
-## [3] rtracklayer_1.36.3 VariantAnnotation_1.22.1
-## [5] SummarizedExperiment_1.6.3 DelayedArray_0.2.7
+## [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.44.2
+## [3] rtracklayer_1.36.6 VariantAnnotation_1.22.3
+## [5] SummarizedExperiment_1.6.5 DelayedArray_0.2.7
## [7] matrixStats_0.52.2 Rsamtools_1.28.0
-## [9] Biostrings_2.44.1 XVector_0.16.0
-## [11] GenomicFeatures_1.28.3 AnnotationDbi_1.38.1
-## [13] Biobase_2.36.2 GenomicRanges_1.28.3
-## [15] GenomeInfoDb_1.12.2 IRanges_2.10.2
-## [17] S4Vectors_0.14.3 AnnotationHub_2.8.2
-## [19] BiocGenerics_0.22.0 BiocStyle_2.4.0
+## [9] Biostrings_2.44.2 XVector_0.16.0
+## [11] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2
+## [13] Biobase_2.36.2 GenomicRanges_1.28.6
+## [15] GenomeInfoDb_1.12.3 IRanges_2.10.5
+## [17] S4Vectors_0.14.7 AnnotationHub_2.8.3
+## [19] BiocGenerics_0.22.1 BiocStyle_2.4.1
##
## loaded via a namespace (and not attached):
-## [1] Rcpp_0.12.11 compiler_3.4.0 BiocInstaller_1.26.0
-## [4] bitops_1.0-6 tools_3.4.0 zlibbioc_1.22.0
-## [7] biomaRt_2.32.1 digest_0.6.12 lattice_0.20-35
-## [10] RSQLite_1.1-2 evaluate_0.10 memoise_1.1.0
-## [13] Matrix_1.2-10 shiny_1.0.3 DBI_0.6-1
-## [16] curl_2.6 yaml_2.1.14 GenomeInfoDbData_0.99.0
-## [19] httr_1.2.1 stringr_1.2.0 knitr_1.16
-## [22] grid_3.4.0 rprojroot_1.2 R6_2.2.1
-## [25] BiocParallel_1.10.1 XML_3.98-1.7 rmarkdown_1.5
-## [28] magrittr_1.5 GenomicAlignments_1.12.1 backports_1.1.0
-## [31] htmltools_0.3.6 mime_0.5 interactiveDisplayBase_1.14.0
-## [34] xtable_1.8-2 httpuv_1.3.3 stringi_1.1.5
-## [37] RCurl_1.95-4.8</code></pre>
+## [1] lattice_0.20-35 htmltools_0.3.6 yaml_2.1.14
+## [4] interactiveDisplayBase_1.14.0 blob_1.1.0 XML_3.98-1.9
+## [7] rlang_0.1.2 DBI_0.7 BiocParallel_1.10.1
+## [10] bit64_0.9-7 GenomeInfoDbData_0.99.0 stringr_1.2.0
+## [13] zlibbioc_1.22.0 memoise_1.1.0 evaluate_0.10.1
+## [16] knitr_1.17 biomaRt_2.32.1 httpuv_1.3.5
+## [19] BiocInstaller_1.26.1 curl_3.0 Rcpp_0.12.13
+## [22] xtable_1.8-2 backports_1.1.1 mime_0.5
+## [25] bit_1.1-12 digest_0.6.12 stringi_1.1.5
+## [28] shiny_1.0.5 rprojroot_1.2 grid_3.4.2
+## [31] tools_3.4.2 bitops_1.0-6 magrittr_1.5
+## [34] RCurl_1.95-4.8 tibble_1.3.4 RSQLite_2.0
+## [37] pkgconfig_2.0.1 Matrix_1.2-11 rmarkdown_1.6
+## [40] httr_1.3.1 R6_2.2.2 GenomicAlignments_1.12.2
+## [43] compiler_3.4.2</code></pre>
</div>
diff --git a/inst/doc/AnnotationHub.html b/inst/doc/AnnotationHub.html
index 95b3998..3e00624 100644
--- a/inst/doc/AnnotationHub.html
+++ b/inst/doc/AnnotationHub.html
@@ -74,7 +74,7 @@ document.addEventListener("DOMContentLoaded", function() {
links[i].target = '_blank';
});
</script>
-<p><strong>Package</strong>: <em><a href="http://bioconductor.org/packages/AnnotationHub">AnnotationHub</a></em><br /> <strong>Authors</strong>: Martin Morgan [cre], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb]<br /> <strong>Modified</strong>: 27 May, 2016<br /> <strong>Compiled</strong>: Sat Jun 10 19:23:30 2017</p>
+<p><strong>Package</strong>: <em><a href="http://bioconductor.org/packages/AnnotationHub">AnnotationHub</a></em><br /> <strong>Authors</strong>: Martin Morgan [cre], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb]<br /> <strong>Modified</strong>: 27 May, 2016<br /> <strong>Compiled</strong>: Tue Oct 17 19:19:56 2017</p>
<p>The <code>AnnotationHub</code> server provides easy <em>R / Bioconductor</em> access to large collections of publicly available whole genome resources, e.g,. ENSEMBL genome fasta or gtf files, UCSC chain resources, ENCODE data tracks at UCSC, etc.</p>
<div id="annotationhub-objects" class="section level1">
<h1><span class="header-section-number">1</span> AnnotationHub objects</h1>
@@ -321,9 +321,9 @@ txdb <- loadDb("/locationToFile/mytxdb.sqlite")</code></pre>
<div id="session-info" class="section level1">
<h1><span class="header-section-number">5</span> Session info</h1>
<pre class="r"><code>sessionInfo()</code></pre>
-<pre><code>## R version 3.4.0 (2017-04-21)
+<pre><code>## R version 3.4.2 (2017-09-28)
## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Ubuntu 16.04.2 LTS
+## Running under: Ubuntu 16.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.5-bioc/R/lib/libRblas.so
@@ -342,37 +342,40 @@ txdb <- loadDb("/locationToFile/mytxdb.sqlite")</code></pre>
## [8] methods base
##
## other attached packages:
-## [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.44.0
-## [3] rtracklayer_1.36.3 VariantAnnotation_1.22.1
-## [5] SummarizedExperiment_1.6.3 DelayedArray_0.2.7
+## [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.44.2
+## [3] rtracklayer_1.36.6 VariantAnnotation_1.22.3
+## [5] SummarizedExperiment_1.6.5 DelayedArray_0.2.7
## [7] matrixStats_0.52.2 Rsamtools_1.28.0
-## [9] Biostrings_2.44.1 XVector_0.16.0
-## [11] GenomicFeatures_1.28.3 AnnotationDbi_1.38.1
-## [13] Biobase_2.36.2 GenomicRanges_1.28.3
-## [15] GenomeInfoDb_1.12.2 IRanges_2.10.2
-## [17] S4Vectors_0.14.3 AnnotationHub_2.8.2
-## [19] BiocGenerics_0.22.0 BiocStyle_2.4.0
+## [9] Biostrings_2.44.2 XVector_0.16.0
+## [11] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2
+## [13] Biobase_2.36.2 GenomicRanges_1.28.6
+## [15] GenomeInfoDb_1.12.3 IRanges_2.10.5
+## [17] S4Vectors_0.14.7 AnnotationHub_2.8.3
+## [19] BiocGenerics_0.22.1 BiocStyle_2.4.1
##
## loaded via a namespace (and not attached):
-## [1] Rcpp_0.12.11 compiler_3.4.0
-## [3] BiocInstaller_1.26.0 bitops_1.0-6
-## [5] tools_3.4.0 zlibbioc_1.22.0
-## [7] biomaRt_2.32.1 digest_0.6.12
-## [9] lattice_0.20-35 RSQLite_1.1-2
-## [11] evaluate_0.10 memoise_1.1.0
-## [13] Matrix_1.2-10 shiny_1.0.3
-## [15] DBI_0.6-1 curl_2.6
-## [17] yaml_2.1.14 GenomeInfoDbData_0.99.0
-## [19] httr_1.2.1 stringr_1.2.0
-## [21] knitr_1.16 grid_3.4.0
-## [23] rprojroot_1.2 R6_2.2.1
-## [25] BiocParallel_1.10.1 XML_3.98-1.7
-## [27] rmarkdown_1.5 magrittr_1.5
-## [29] GenomicAlignments_1.12.1 backports_1.1.0
-## [31] htmltools_0.3.6 mime_0.5
-## [33] interactiveDisplayBase_1.14.0 xtable_1.8-2
-## [35] httpuv_1.3.3 stringi_1.1.5
-## [37] RCurl_1.95-4.8</code></pre>
+## [1] lattice_0.20-35 htmltools_0.3.6
+## [3] yaml_2.1.14 interactiveDisplayBase_1.14.0
+## [5] blob_1.1.0 XML_3.98-1.9
+## [7] rlang_0.1.2 DBI_0.7
+## [9] BiocParallel_1.10.1 bit64_0.9-7
+## [11] GenomeInfoDbData_0.99.0 stringr_1.2.0
+## [13] zlibbioc_1.22.0 memoise_1.1.0
+## [15] evaluate_0.10.1 knitr_1.17
+## [17] biomaRt_2.32.1 httpuv_1.3.5
+## [19] BiocInstaller_1.26.1 curl_3.0
+## [21] Rcpp_0.12.13 xtable_1.8-2
+## [23] backports_1.1.1 mime_0.5
+## [25] bit_1.1-12 digest_0.6.12
+## [27] stringi_1.1.5 shiny_1.0.5
+## [29] rprojroot_1.2 grid_3.4.2
+## [31] tools_3.4.2 bitops_1.0-6
+## [33] magrittr_1.5 RCurl_1.95-4.8
+## [35] tibble_1.3.4 RSQLite_2.0
+## [37] pkgconfig_2.0.1 Matrix_1.2-11
+## [39] rmarkdown_1.6 httr_1.3.1
+## [41] R6_2.2.2 GenomicAlignments_1.12.2
+## [43] compiler_3.4.2</code></pre>
</div>
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