Add a bunch of deprules

5 files changed, 66 insertions, 20 deletions

diff --git a/config/simple-deprules.d/dot_remap b/config/simple-deprules.d/dot_remap
index 57d65b1..9b53f32 100644
--- a/config/simple-deprules.d/dot_remap
+++ b/config/simple-deprules.d/dot_remap
@@ -49,6 +49,27 @@
 ~sci-R/oro_dicom :: oro.dicom
 ~sci-R/oro_nifti :: oro.nifti
 
+~sci-R/org_Ag_eg_db :: org.Ag.eg.db
+~sci-R/org_At_tair_db :: org.At.tair.db
+~sci-R/org_Bt_eg_db :: org.Bt.eg.db
+~sci-R/org_Ce_eg_db :: org.Ce.eg.db
+~sci-R/org_Cf_eg_db :: org.Cf.eg.db
+~sci-R/org_Dm_eg_db :: org.Dm.eg.db
+~sci-R/org_Dr_eg_db :: org.Dr.eg.db
+~sci-R/org_EcK12_eg_db :: org.EcK12.eg.db
+~sci-R/org_EcSakai_eg_db :: org.EcSakai.eg.db
+~sci-R/org_Gg_eg_db :: org.Gg.eg.db
+~sci-R/org_Hs_eg_db :: org.Hs.eg.db
+~sci-R/org_Mm_eg_db :: org.Mm.eg.db
+~sci-R/org_Mmu_eg_db :: org.Mmu.eg.db
+~sci-R/org_Pf_plasmo_db :: org.Pf.plasmo.db
+~sci-R/org_Pt_eg_db :: org.Pt.eg.db
+~sci-R/org_Rn_eg_db :: org.Rn.eg.db
+~sci-R/org_Sc_sgd_db :: org.Sc.sgd.db
+~sci-R/org_Sco_eg_db :: org.Sco.eg.db
+~sci-R/org_Ss_eg_db :: org.Ss.eg.db
+~sci-R/org_Xl_eg_db :: org.Xl.eg.db
+
 ~sci-R/R_cache :: R.cache
 ~sci-R/RcmdrPlugin_IPSUR :: RcmdrPlugin.IPSUR
 ~sci-R/R_devices :: R.devices
@@ -70,3 +91,38 @@
 ~sci-R/survJamda_data :: survJamda.data
 
 ~sci-R/tawny_types :: tawny.types
+
+~sci-R/DO_db :: DO.db
+~sci-R/IlluminaHumanMethylation27k_db :: IlluminaHumanMethylation27k.db
+~sci-R/IlluminaHumanMethylation450k_db :: IlluminaHumanMethylation450k.db
+~sci-R/KEGG_db :: KEGG.db
+~sci-R/SNPlocs_Hsapiens_dbSNP_20090506 :: SNPlocs.Hsapiens.dbSNP.20090506
+~sci-R/SNPlocs_Hsapiens_dbSNP_20100427 :: SNPlocs.Hsapiens.dbSNP.20100427
+~sci-R/SNPlocs_Hsapiens_dbSNP_20101109 :: SNPlocs.Hsapiens.dbSNP.20101109
+~sci-R/gahgu133plus2_db :: gahgu133plus2.db
+~sci-R/hgfocus_db :: hgfocus.db
+~sci-R/hgu133a_db :: hgu133a.db
+~sci-R/hgu133plus2_db :: hgu133plus2.db
+~sci-R/hgu95a_db :: hgu95a.db
+~sci-R/hgu95av2_db :: hgu95av2.db
+~sci-R/hgug4112a_db :: hgug4112a.db
+~sci-R/hu6800_db :: hu6800.db
+~sci-R/illuminaHumanv1_db :: illuminaHumanv1.db
+~sci-R/nutshell_bbdb :: nutshell.bbdb
+~sci-R/reactome_db :: reactome.db
+
+~sci-R/RmiR_Hs_miRNA :: RmiR.Hs.miRNA
+~sci-R/TxDb_Hsapiens_UCSC_hg18_knownGene :: TxDb.Hsapiens.UCSC.hg18.knownGene
+~sci-R/TxDb_Hsapiens_UCSC_hg19_knownGene :: TxDb.Hsapiens.UCSC.hg19.knownGene
+~sci-R/bigmemory_sri :: bigmemory.sri
+~sci-R/gamlss_add :: gamlss.add
+~sci-R/gemtc_jar :: gemtc.jar
+~sci-R/haplo_stats :: haplo.stats
+~sci-R/nutshell_audioscrobbler :: nutshell.audioscrobbler
+~sci-R/pd_charm_hg18_example :: pd.charm.hg18.example
+~sci-R/pd_mapping250k_nsp :: pd.mapping250k.nsp
+~sci-R/pd_mapping250k_sty :: pd.mapping250k.sty
+~sci-R/pd_mapping50k_hind240 :: pd.mapping50k.hind240
+~sci-R/pd_mapping50k_xba240 :: pd.mapping50k.xba240
+~sci-R/simdat_base :: simdat.base
+
diff --git a/config/simple-deprules.d/ignored_text b/config/simple-deprules.d/ignored_text
index 31871e3..34f11eb 100644
--- a/config/simple-deprules.d/ignored_text
+++ b/config/simple-deprules.d/ignored_text
@@ -57,3 +57,6 @@
 	windows: Tiff(libtiff3.dll)
 	zlib1.dll and jpeg62.dll
 }
+
+# typo, and glibc is always built with pthreads nowadays
+! :: lippthread
diff --git a/config/simple-deprules.d/missing b/config/simple-deprules.d/missing
index 0cf60b4..9674bba 100644
--- a/config/simple-deprules.d/missing
+++ b/config/simple-deprules.d/missing
@@ -243,26 +243,6 @@ moe430a.db,
 mogene10sttranscriptcluster.db,
 mouse.db0 -- BIOC
 "mSQL-2.0.8 (http://www.Hughes.com.au), mSQL-2.0.8 (http://www.Hughes.com.au) or higher" --
-org.Ag.eg.db,
-org.At.tair.db,
-org.Bt.eg.db,
-org.Ce.eg.db,
-org.Cf.eg.db,
-org.Dm.eg.db,
-org.Dr.eg.db,
-org.EcK12.eg.db,
-org.EcSakai.eg.db,
-org.Gg.eg.db,
-org.Hs.eg.db,
-org.Hs.ipi.db,
-org.Mm.eg.db,
-org.Mmu.eg.db,
-org.Pf.plasmo.db,
-org.Pt.eg.db,
-org.Rn.eg.db,
-org.Sco.eg.db,
-org.Sc.sgd.db,
-org.Ss.eg.db,
 org.Xl.eg.db -- BIOC
 pcaGoPromoter.Hs.hg19,
 pcaGoPromoter.Mm.mm9,
diff --git a/config/simple-deprules.d/sci-libs b/config/simple-deprules.d/sci-libs
index 8e20c5b..cb48d04 100644
--- a/config/simple-deprules.d/sci-libs
+++ b/config/simple-deprules.d/sci-libs
@@ -74,3 +74,6 @@ sci-libs/udunits :: udunits (>= 1.11.7) or udunits2(>= 2.1.22)
 }
 
 virtual/blas :: blas
+
+# In the science overlay
+~sci-libs/coinor-clp :: COIN-OR Clp
diff --git a/config/simple-deprules.d/sys b/config/simple-deprules.d/sys
index 3b793d0..df2ad0c 100644
--- a/config/simple-deprules.d/sys
+++ b/config/simple-deprules.d/sys
@@ -14,3 +14,7 @@ sys-libs/zlib :: zlib (optional)
 	LamMPI(>= 6.5.9) or MPICH2(>= 1.0.2) or OpenMPI ()
 	LamMpi(>= 6.5.9) or Mpich2(>= 1.0.2)
 }
+
+! {
+	rgl packages for rendering
+}