diff options
| -rw-r--r-- | .SRCINFO | 16 | ||||
| -rw-r--r-- | PKGBUILD | 14 | ||||
| -rw-r--r-- | fix-test-snapshot.patch | 64 |
3 files changed, 79 insertions, 15 deletions
@@ -1,10 +1,10 @@ pkgbase = r-mariner pkgdesc = Explore the Hi-Cs - pkgver = 1.2.0 - pkgrel = 2 + pkgver = 1.4.0 + pkgrel = 1 url = https://bioconductor.org/packages/mariner arch = any - license = GPL3 + license = GPL-3.0-only checkdepends = r-marinerdata checkdepends = r-testthat depends = r-abind @@ -39,11 +39,11 @@ pkgbase = r-mariner optdepends = r-marinerdata optdepends = r-rmarkdown optdepends = r-testthat - source = https://bioconductor.org/packages/release/bioc/src/contrib/mariner_1.2.0.tar.gz + source = https://bioconductor.org/packages/release/bioc/src/contrib/mariner_1.4.0.tar.gz source = fix-test-snapshot.patch - md5sums = 6ed30878d03b8a17e8e7c4ee17218893 - md5sums = d0928c3ea11234e2200f31c9b4ff4ade - b2sums = dfaa195e26df395d9948668e342bcc5bc2c593d42b102a7140cb6778fc904f171b561c7fe1d6bce1dbefbd22832b745888549f06eff42c5596455d48e2693db3 - b2sums = aba583ffb72fea9e7ce5820b8160418b345b87e1d93fe9533efeb5732011373bd18dfea4c16b49f869e0d698529f48f738bec528c77d67c1cf095e7656a6ca30 + md5sums = 59fce5faa48236d0a9cd9bdda6480d3d + md5sums = b055713d876d7ea3e97a92a152bb5f28 + b2sums = e2c553258972c7d24b907feab042be3fce9547636a6fbb1c264148002928b48fec581504e8281c214d076bdca3933eda08f9df6ad6f7b0d74d1e3847e8bee75f + b2sums = 6111457fda4b526e70b08ac62ec1ffd68dd8fe81d6d57cd715ef4f10a5156756d788043a924d9b3103958775cc28d02e0313947187a571907a9f6adf879148a1 pkgname = r-mariner @@ -1,14 +1,14 @@ # Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com> _pkgname=mariner -_pkgver=1.2.0 +_pkgver=1.4.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} -pkgrel=2 +pkgrel=1 pkgdesc="Explore the Hi-Cs" arch=(any) url="https://bioconductor.org/packages/$_pkgname" -license=(GPL3) +license=('GPL-3.0-only') depends=( r-abind r-assertthat @@ -51,10 +51,10 @@ optdepends=( ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz" "fix-test-snapshot.patch") -md5sums=('6ed30878d03b8a17e8e7c4ee17218893' - 'd0928c3ea11234e2200f31c9b4ff4ade') -b2sums=('dfaa195e26df395d9948668e342bcc5bc2c593d42b102a7140cb6778fc904f171b561c7fe1d6bce1dbefbd22832b745888549f06eff42c5596455d48e2693db3' - 'aba583ffb72fea9e7ce5820b8160418b345b87e1d93fe9533efeb5732011373bd18dfea4c16b49f869e0d698529f48f738bec528c77d67c1cf095e7656a6ca30') +md5sums=('59fce5faa48236d0a9cd9bdda6480d3d' + 'b055713d876d7ea3e97a92a152bb5f28') +b2sums=('e2c553258972c7d24b907feab042be3fce9547636a6fbb1c264148002928b48fec581504e8281c214d076bdca3933eda08f9df6ad6f7b0d74d1e3847e8bee75f' + '6111457fda4b526e70b08ac62ec1ffd68dd8fe81d6d57cd715ef4f10a5156756d788043a924d9b3103958775cc28d02e0313947187a571907a9f6adf879148a1') prepare() { # fix snapshot test diff --git a/fix-test-snapshot.patch b/fix-test-snapshot.patch index 9359df6e98fe..98f0098be528 100644 --- a/fix-test-snapshot.patch +++ b/fix-test-snapshot.patch @@ -65,3 +65,67 @@ index 492df25..e6645e7 100644 ,,1,FS [,1] [,2] [,3] ... [,10] [,11] [1,] 0 0 0 . 0 0 +diff --git a/mariner/tests/testthat/_snaps/MergedGInteractions.md b/mariner/tests/testthat/_snaps/MergedGInteractions.md +index f27c0ed..999e149 100644 +--- a/mariner/tests/testthat/_snaps/MergedGInteractions.md ++++ b/mariner/tests/testthat/_snaps/MergedGInteractions.md +@@ -4,6 +4,7 @@ + .mapIds(x) + Output + seqnames1 start1 end1 width1 strand1 seqnames2 start2 end2 ++ <fctr> <int> <int> <int> <fctr> <fctr> <int> <int> + 1: chr9 118645000 118650000 5001 * chr9 119330000 119335000 + 2: chr9 118645000 118650000 5001 * chr9 119330000 119335000 + 3: chr17 80635000 80640000 5001 * chr17 80920000 80925000 +@@ -12,16 +13,18 @@ + 6: chr9 14460000 14465000 5001 * chr9 14765000 14770000 + 7: chr17 47645000 47650000 5001 * chr17 48075000 48080000 + 8: chr17 47645000 47650000 5001 * chr17 48075000 48080000 +- width2 strand2 color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg +- 1: 5001 * 0,0,0 2.611034 0.9860443 1.414376 +- 2: 5001 * 0,0,0 2.611034 0.9860443 1.414376 +- 3: 5001 * 0,0,0 2.889573 0.9713564 1.379367 +- 4: 5001 * 0,0,0 2.889573 0.9713564 1.379367 +- 5: 5001 * 0,0,0 3.272132 0.9868535 2.233533 +- 6: 5001 * 0,0,0 3.272132 0.9868535 2.233533 +- 7: 5001 * 0,0,0 3.520431 0.9801694 2.433166 +- 8: 5001 * 0,0,0 3.520431 0.9801694 2.433166 ++ width2 strand2 color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg ++ <int> <fctr> <char> <num> <num> <num> ++ 1: 5001 * 0,0,0 2.611034 0.9860443 1.414376 ++ 2: 5001 * 0,0,0 2.611034 0.9860443 1.414376 ++ 3: 5001 * 0,0,0 2.889573 0.9713564 1.379367 ++ 4: 5001 * 0,0,0 2.889573 0.9713564 1.379367 ++ 5: 5001 * 0,0,0 3.272132 0.9868535 2.233533 ++ 6: 5001 * 0,0,0 3.272132 0.9868535 2.233533 ++ 7: 5001 * 0,0,0 3.520431 0.9801694 2.433166 ++ 8: 5001 * 0,0,0 3.520431 0.9801694 2.433166 + Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std value ++ <num> <num> <num> <num> <num> + 1: 1.8755854 2.121637 2.605124 0.7942202 4.272311 + 2: 1.8755854 2.121637 2.605124 0.7942202 4.272311 + 3: 1.9105295 1.946362 1.854944 0.6729783 3.553193 +@@ -30,13 +33,14 @@ + 6: 1.0059373 1.645508 3.437883 0.5164226 4.332049 + 7: 0.8104557 1.486894 3.200528 0.6733462 3.920933 + 8: 0.8104557 1.486894 3.200528 0.6733462 3.920933 +- src id grp clst i.id +- 1: FS 1 1 1 1 +- 2: FS 5 1 1 1 +- 3: FS 2 2 1 2 +- 4: FS 6 2 1 2 +- 5: WT 3 1 2 3 +- 6: WT 7 1 2 3 +- 7: WT 4 2 2 4 +- 8: WT 8 2 2 4 ++ src id grp clst i.id ++ <char> <int> <int> <int> <int> ++ 1: FS 1 1 1 1 ++ 2: FS 5 1 1 1 ++ 3: FS 2 2 1 2 ++ 4: FS 6 2 1 2 ++ 5: WT 3 1 2 3 ++ 6: WT 7 1 2 3 ++ 7: WT 4 2 2 4 ++ 8: WT 8 2 2 4 + |