From 6f9124e11860095d90515e7fb8f702f1779b3fe8 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 17:11:23 +0100
Subject: [PATCH 01/53] r-modules: fix Cairo package

---
 pkgs/development/r-modules/default.nix | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 093bc2f78848..529c6db091d3 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -247,7 +247,7 @@ let
     bnpmr = [ pkgs.gsl_1 ];
     BNSP = [ pkgs.gsl_1 ];
     cairoDevice = [ pkgs.gtk2 ];
-    Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
+    Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ];
     Cardinal = [ pkgs.which ];
     chebpol = [ pkgs.fftw ];
     ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
@@ -1791,6 +1791,10 @@ let
         '';
     });
 
+    Cairo = old.Cairo.overrideDerivation (attrs: {
+      NIX_LDFLAGS = "-lfontconfig";
+    });
+
     curl = old.curl.overrideDerivation (attrs: {
       preConfigure = "patchShebangs configure";
     });

From 88fcfafafe33625edefc5b195ce5fd744ba72d95 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 17:30:04 +0100
Subject: [PATCH 02/53] r-modules: fix BayesXsrc package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 529c6db091d3..6f1807b4138f 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -240,7 +240,7 @@ let
     audio = [ pkgs.portaudio ];
     BayesSAE = [ pkgs.gsl_1 ];
     BayesVarSel = [ pkgs.gsl_1 ];
-    BayesXsrc = [ pkgs.readline pkgs.ncurses ];
+    BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ];
     bigGP = [ pkgs.openmpi ];
     BiocCheck = [ pkgs.which ];
     Biostrings = [ pkgs.zlib ];

From f7175388663e600b792c1c22a5b0ba887a7c45aa Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 17:34:21 +0100
Subject: [PATCH 03/53] r-modules: fix git2r package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 6f1807b4138f..64e889d76127 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -260,7 +260,7 @@ let
     fftwtools = [ pkgs.fftw ];
     Formula = [ pkgs.gmp ];
     geoCount = [ pkgs.gsl_1 ];
-    git2r = [ pkgs.zlib pkgs.openssl ];
+    git2r = [ pkgs.zlib.dev pkgs.openssl.dev ];
     GLAD = [ pkgs.gsl_1 ];
     glpkAPI = [ pkgs.gmp pkgs.glpk ];
     gmp = [ pkgs.gmp ];

From 6c6aab3e5b545d4d58c80b29c839f23e0f86fa73 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 17:41:42 +0100
Subject: [PATCH 04/53] r-modules: fix cairoDevice package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 64e889d76127..29859f375091 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -246,7 +246,7 @@ let
     Biostrings = [ pkgs.zlib ];
     bnpmr = [ pkgs.gsl_1 ];
     BNSP = [ pkgs.gsl_1 ];
-    cairoDevice = [ pkgs.gtk2 ];
+    cairoDevice = [ pkgs.gtk2.dev ];
     Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ];
     Cardinal = [ pkgs.which ];
     chebpol = [ pkgs.fftw ];

From b88b8ea05b530170a355798ec44940490cb0352f Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 17:58:58 +0100
Subject: [PATCH 05/53] r-modules: fix devEMF package

---
 pkgs/development/r-modules/default.nix | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 29859f375091..16c6d22eeeb2 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -253,7 +253,7 @@ let
     ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
     cit = [ pkgs.gsl_1 ];
     curl = [ pkgs.curl.dev ];
-    devEMF = [ pkgs.xorg.libXft ];
+    devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ];
     diversitree = [ pkgs.gsl_1 pkgs.fftw ];
     EMCluster = [ pkgs.liblapack ];
     fftw = [ pkgs.fftw ];
@@ -1863,6 +1863,7 @@ let
 
     devEMF = old.devEMF.overrideDerivation (attrs: {
       NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft";
+      NIX_LDFLAGS = "-lX11";
     });
 
     slfm = old.slfm.overrideDerivation (attrs: {

From 427c4d954a0c1c4447fd6ee3973de6eafe71699d Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 18:15:14 +0100
Subject: [PATCH 06/53] r-modules: fix fftw package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 16c6d22eeeb2..d47479105232 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -256,7 +256,7 @@ let
     devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ];
     diversitree = [ pkgs.gsl_1 pkgs.fftw ];
     EMCluster = [ pkgs.liblapack ];
-    fftw = [ pkgs.fftw ];
+    fftw = [ pkgs.fftw.dev ];
     fftwtools = [ pkgs.fftw ];
     Formula = [ pkgs.gmp ];
     geoCount = [ pkgs.gsl_1 ];

From 72eb6a8644ec073bf0a2fc9556388922a9e78c19 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 18:16:44 +0100
Subject: [PATCH 07/53] r-modules: fix fftwtools package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index d47479105232..96d0d8af4574 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -257,7 +257,7 @@ let
     diversitree = [ pkgs.gsl_1 pkgs.fftw ];
     EMCluster = [ pkgs.liblapack ];
     fftw = [ pkgs.fftw.dev ];
-    fftwtools = [ pkgs.fftw ];
+    fftwtools = [ pkgs.fftw.dev ];
     Formula = [ pkgs.gmp ];
     geoCount = [ pkgs.gsl_1 ];
     git2r = [ pkgs.zlib.dev pkgs.openssl.dev ];

From e3a2c97c7b8cdb783cd655cc6d093ff539d47b2b Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 18:20:41 +0100
Subject: [PATCH 08/53] r-modules: fix gmp package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 96d0d8af4574..37c6b4e81347 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -263,7 +263,7 @@ let
     git2r = [ pkgs.zlib.dev pkgs.openssl.dev ];
     GLAD = [ pkgs.gsl_1 ];
     glpkAPI = [ pkgs.gmp pkgs.glpk ];
-    gmp = [ pkgs.gmp ];
+    gmp = [ pkgs.gmp.dev ];
     graphscan = [ pkgs.gsl_1 ];
     gsl = [ pkgs.gsl_1 ];
     h5 = [ pkgs.hdf5-cpp pkgs.which ];

From debb12ce1a5e06fb2348746ac34c1dbc8567a496 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:17:19 +0100
Subject: [PATCH 09/53] r-module: fix jpeg package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 37c6b4e81347..509dba07f982 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -272,7 +272,7 @@ let
     iBMQ = [ pkgs.gsl_1 ];
     igraph = [ pkgs.gmp ];
     JavaGD = [ pkgs.jdk ];
-    jpeg = [ pkgs.libjpeg ];
+    jpeg = [ pkgs.libjpeg.dev ];
     KFKSDS = [ pkgs.gsl_1 ];
     kza = [ pkgs.fftw ];
     libamtrack = [ pkgs.gsl_1 ];

From 4e7de52c26580f9bad962d2507bc1239df4abffd Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:18:27 +0100
Subject: [PATCH 10/53] r-module: fix kza package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 509dba07f982..a81fc649a46a 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -274,7 +274,7 @@ let
     JavaGD = [ pkgs.jdk ];
     jpeg = [ pkgs.libjpeg.dev ];
     KFKSDS = [ pkgs.gsl_1 ];
-    kza = [ pkgs.fftw ];
+    kza = [ pkgs.fftw.dev ];
     libamtrack = [ pkgs.gsl_1 ];
     mixcat = [ pkgs.gsl_1 ];
     mvabund = [ pkgs.gsl_1 ];

From 1e9071948f646be2d459fbb2403619a8c6ddffbb Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:19:27 +0100
Subject: [PATCH 11/53] r-modules: fix mwaved package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index a81fc649a46a..3e3bb65d1bb8 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -278,7 +278,7 @@ let
     libamtrack = [ pkgs.gsl_1 ];
     mixcat = [ pkgs.gsl_1 ];
     mvabund = [ pkgs.gsl_1 ];
-    mwaved = [ pkgs.fftw ];
+    mwaved = [ pkgs.fftw.dev ];
     ncdf4 = [ pkgs.netcdf ];
     nloptr = [ pkgs.nlopt ];
     openssl = [ pkgs.openssl.dev ];

From c5ef08cc655bab0f06c0f81402e64b87269593e0 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:23:42 +0100
Subject: [PATCH 12/53] r-modules: fix PKI package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 3e3bb65d1bb8..07070a6e775c 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -287,7 +287,7 @@ let
     pbdMPI = [ pkgs.openmpi ];
     pbdNCDF4 = [ pkgs.netcdf ];
     pbdPROF = [ pkgs.openmpi ];
-    PKI = [ pkgs.openssl ];
+    PKI = [ pkgs.openssl.dev ];
     png = [ pkgs.libpng.dev ];
     PopGenome = [ pkgs.zlib ];
     proj4 = [ pkgs.proj ];

From 062c9037d144ae4b7c49f6d4212a994485d4aa6a Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:25:06 +0100
Subject: [PATCH 13/53] r-modules: fix PopGenome package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 07070a6e775c..193b8b7baac8 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -289,7 +289,7 @@ let
     pbdPROF = [ pkgs.openmpi ];
     PKI = [ pkgs.openssl.dev ];
     png = [ pkgs.libpng.dev ];
-    PopGenome = [ pkgs.zlib ];
+    PopGenome = [ pkgs.zlib.dev ];
     proj4 = [ pkgs.proj ];
     qtbase = [ pkgs.qt4 ];
     qtpaint = [ pkgs.qt4 ];

From 277efe9896d805ac1fa98d69cc0c4a480533b83b Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:27:45 +0100
Subject: [PATCH 14/53] r-modules: fix sysfonts package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 193b8b7baac8..c861f29223f4 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -352,7 +352,7 @@ let
     stsm = [ pkgs.gsl_1 ];
     stringi = [ pkgs.icu.dev ];
     survSNP = [ pkgs.gsl_1 ];
-    sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
+    sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
     TAQMNGR = [ pkgs.zlib ];
     tiff = [ pkgs.libtiff ];
     TKF = [ pkgs.gsl_1 ];

From 558f67e85f93268f172d3b30439a66fe221f87ac Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:30:56 +0100
Subject: [PATCH 15/53] r-modules: fix R2SWF package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index c861f29223f4..f5b4009dd854 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -294,7 +294,7 @@ let
     qtbase = [ pkgs.qt4 ];
     qtpaint = [ pkgs.qt4 ];
     R2GUESS = [ pkgs.gsl_1 ];
-    R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
+    R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
     RAppArmor = [ pkgs.libapparmor ];
     rapportools = [ pkgs.which ];
     rapport = [ pkgs.which ];

From 8b229baf334cb0df5a691523206ea6df914bcabf Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:33:45 +0100
Subject: [PATCH 16/53] r-modules: fix rbamtools package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index f5b4009dd854..45645e87c27f 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -298,7 +298,7 @@ let
     RAppArmor = [ pkgs.libapparmor ];
     rapportools = [ pkgs.which ];
     rapport = [ pkgs.which ];
-    rbamtools = [ pkgs.zlib ];
+    rbamtools = [ pkgs.zlib.dev ];
     rcdd = [ pkgs.gmp ];
     RcppCNPy = [ pkgs.zlib ];
     RcppGSL = [ pkgs.gsl_1 ];

From dd159d06b6c793fb6f06c3b4bb5267f314b8e614 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:34:30 +0100
Subject: [PATCH 17/53] r-modules: fix rcdd package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 45645e87c27f..c7ac571ce4c2 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -299,7 +299,7 @@ let
     rapportools = [ pkgs.which ];
     rapport = [ pkgs.which ];
     rbamtools = [ pkgs.zlib.dev ];
-    rcdd = [ pkgs.gmp ];
+    rcdd = [ pkgs.gmp.dev ];
     RcppCNPy = [ pkgs.zlib ];
     RcppGSL = [ pkgs.gsl_1 ];
     RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];

From ba86a3964566cbefdd1badcad84c5054f84604ea Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:35:20 +0100
Subject: [PATCH 18/53] r-modules: fix RcppCNPy package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index c7ac571ce4c2..1908c08d52c1 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -300,7 +300,7 @@ let
     rapport = [ pkgs.which ];
     rbamtools = [ pkgs.zlib.dev ];
     rcdd = [ pkgs.gmp.dev ];
-    RcppCNPy = [ pkgs.zlib ];
+    RcppCNPy = [ pkgs.zlib.dev ];
     RcppGSL = [ pkgs.gsl_1 ];
     RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
     RcppZiggurat = [ pkgs.gsl_1 ];

From 3342f8bd59728902c915434d215492587100cd2e Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:38:00 +0100
Subject: [PATCH 19/53] r-modules: fix RcppOctave package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 1908c08d52c1..b79d945d2a93 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -302,7 +302,7 @@ let
     rcdd = [ pkgs.gmp.dev ];
     RcppCNPy = [ pkgs.zlib.dev ];
     RcppGSL = [ pkgs.gsl_1 ];
-    RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
+    RcppOctave = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.octave ];
     RcppZiggurat = [ pkgs.gsl_1 ];
     rgdal = [ pkgs.proj pkgs.gdal ];
     rgeos = [ pkgs.geos ];

From 9f2b5e0425c1cde3594ffc274ea07c343554a749 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:51:28 +0100
Subject: [PATCH 20/53] r-modules: fix RGtk2 package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index b79d945d2a93..65d1dcd6bc26 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -309,7 +309,7 @@ let
     rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ];
     rgl = [ pkgs.mesa pkgs.xlibsWrapper ];
     Rglpk = [ pkgs.glpk ];
-    RGtk2 = [ pkgs.gtk2 ];
+    RGtk2 = [ pkgs.gtk2.dev ];
     rhdf5 = [ pkgs.zlib ];
     Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
     Rhtslib = [ pkgs.zlib ];

From e1bc505da9a5c2b292929937c5fea59c8b9ab064 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:54:01 +0100
Subject: [PATCH 21/53] r-modules: fix rggobi package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 65d1dcd6bc26..a5fe9b5cd905 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -306,7 +306,7 @@ let
     RcppZiggurat = [ pkgs.gsl_1 ];
     rgdal = [ pkgs.proj pkgs.gdal ];
     rgeos = [ pkgs.geos ];
-    rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ];
+    rggobi = [ pkgs.ggobi pkgs.gtk2.dev pkgs.libxml2.dev ];
     rgl = [ pkgs.mesa pkgs.xlibsWrapper ];
     Rglpk = [ pkgs.glpk ];
     RGtk2 = [ pkgs.gtk2.dev ];

From bb60f939aeb108ab4bdfbfa5fddfc403168e22e4 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:56:22 +0100
Subject: [PATCH 22/53] r-modules: fix Rhpc package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index a5fe9b5cd905..8ea725401ebc 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -311,7 +311,7 @@ let
     Rglpk = [ pkgs.glpk ];
     RGtk2 = [ pkgs.gtk2.dev ];
     rhdf5 = [ pkgs.zlib ];
-    Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
+    Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ];
     Rhtslib = [ pkgs.zlib ];
     RJaCGH = [ pkgs.zlib ];
     rjags = [ pkgs.jags ];

From 9922867fa889ec8b5ebd8b8ac39bc6effcdaeb30 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:57:30 +0100
Subject: [PATCH 23/53] r-modules: fix Rhtslib package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 8ea725401ebc..9e4952dc54a5 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -312,7 +312,7 @@ let
     RGtk2 = [ pkgs.gtk2.dev ];
     rhdf5 = [ pkgs.zlib ];
     Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ];
-    Rhtslib = [ pkgs.zlib ];
+    Rhtslib = [ pkgs.zlib.dev ];
     RJaCGH = [ pkgs.zlib ];
     rjags = [ pkgs.jags ];
     rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];

From 13a582688f3358381820d17bdceef5670ee97585 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 19:59:17 +0100
Subject: [PATCH 24/53] r-modules: fix RJaCGH package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 9e4952dc54a5..d1ce64aad040 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -313,7 +313,7 @@ let
     rhdf5 = [ pkgs.zlib ];
     Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ];
     Rhtslib = [ pkgs.zlib.dev ];
-    RJaCGH = [ pkgs.zlib ];
+    RJaCGH = [ pkgs.zlib.dev ];
     rjags = [ pkgs.jags ];
     rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
     Rlibeemd = [ pkgs.gsl_1 ];

From 674a2077dd10600e2f56c0824a0d0a0f5456e0ec Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:00:33 +0100
Subject: [PATCH 25/53] r-modules: fix rJava package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index d1ce64aad040..5d8ed3769a67 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -315,7 +315,7 @@ let
     Rhtslib = [ pkgs.zlib.dev ];
     RJaCGH = [ pkgs.zlib.dev ];
     rjags = [ pkgs.jags ];
-    rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
+    rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
     Rlibeemd = [ pkgs.gsl_1 ];
     rmatio = [ pkgs.zlib ];
     Rmpfr = [ pkgs.gmp pkgs.mpfr ];

From a58db75ccb51734a3e345c48017438a25b015645 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:01:17 +0100
Subject: [PATCH 26/53] r-modules: fix rmatio package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 5d8ed3769a67..3765c88119ed 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -317,7 +317,7 @@ let
     rjags = [ pkgs.jags ];
     rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
     Rlibeemd = [ pkgs.gsl_1 ];
-    rmatio = [ pkgs.zlib ];
+    rmatio = [ pkgs.zlib.dev ];
     Rmpfr = [ pkgs.gmp pkgs.mpfr ];
     Rmpi = [ pkgs.openmpi ];
     RMySQL = [ pkgs.zlib pkgs.mysql.lib ];

From 780fb79e32671e18c9fcdbe6b6a06b87e69a9a62 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:02:17 +0100
Subject: [PATCH 27/53] r-modules: fix Rmpfr package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 3765c88119ed..a669d08381b3 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -318,7 +318,7 @@ let
     rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
     Rlibeemd = [ pkgs.gsl_1 ];
     rmatio = [ pkgs.zlib.dev ];
-    Rmpfr = [ pkgs.gmp pkgs.mpfr ];
+    Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
     Rmpi = [ pkgs.openmpi ];
     RMySQL = [ pkgs.zlib pkgs.mysql.lib ];
     RNetCDF = [ pkgs.netcdf pkgs.udunits ];

From 53235dbe1487264c9785e6357b6f40ab5a2fa5b8 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:06:44 +0100
Subject: [PATCH 28/53] r-modules: fix rphast package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index a669d08381b3..2014192ce94e 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -325,7 +325,7 @@ let
     RODBCext = [ pkgs.libiodbc ];
     RODBC = [ pkgs.libiodbc ];
     rpg = [ pkgs.postgresql ];
-    rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
+    rphast = [ pkgs.pcre.dev pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
     Rpoppler = [ pkgs.poppler ];
     RPostgreSQL = [ pkgs.postgresql ];
     RProtoBuf = [ pkgs.protobuf ];

From bd2aaada6eac1f68a2790737c5b85d037040ae00 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:09:43 +0100
Subject: [PATCH 29/53] r-modules: fix RSclient package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 2014192ce94e..293cdbaa7d2c 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -330,7 +330,7 @@ let
     RPostgreSQL = [ pkgs.postgresql ];
     RProtoBuf = [ pkgs.protobuf ];
     rPython = [ pkgs.python ];
-    RSclient = [ pkgs.openssl ];
+    RSclient = [ pkgs.openssl.dev ];
     Rserve = [ pkgs.openssl ];
     Rssa = [ pkgs.fftw ];
     rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ];

From fd175e4084d961c7466be90d2723da646a6397f4 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:13:30 +0100
Subject: [PATCH 30/53] r-modules: fix Rssa package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 293cdbaa7d2c..4ab142891c43 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -332,7 +332,7 @@ let
     rPython = [ pkgs.python ];
     RSclient = [ pkgs.openssl.dev ];
     Rserve = [ pkgs.openssl ];
-    Rssa = [ pkgs.fftw ];
+    Rssa = [ pkgs.fftw.dev ];
     rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ];
     rtiff = [ pkgs.libtiff ];
     runjags = [ pkgs.jags ];

From d7ac90dd0c7a5169ff570fce1d672c43365b1571 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:16:49 +0100
Subject: [PATCH 31/53] r-modules: fix rtfbs package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 4ab142891c43..6802bd1d539b 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -333,7 +333,7 @@ let
     RSclient = [ pkgs.openssl.dev ];
     Rserve = [ pkgs.openssl ];
     Rssa = [ pkgs.fftw.dev ];
-    rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ];
+    rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ];
     rtiff = [ pkgs.libtiff ];
     runjags = [ pkgs.jags ];
     RVowpalWabbit = [ pkgs.zlib pkgs.boost ];

From ae2723a1442e698ec74d9eca09ced7e0ce9c5a77 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:17:42 +0100
Subject: [PATCH 32/53] r-modules: fix rtiff package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 6802bd1d539b..ed1e276dbbbd 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -334,7 +334,7 @@ let
     Rserve = [ pkgs.openssl ];
     Rssa = [ pkgs.fftw.dev ];
     rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ];
-    rtiff = [ pkgs.libtiff ];
+    rtiff = [ pkgs.libtiff.dev ];
     runjags = [ pkgs.jags ];
     RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
     rzmq = [ pkgs.zeromq3 ];

From 1ef67b9e781efd72aebeb8db1507a10e4e6adbae Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:22:07 +0100
Subject: [PATCH 33/53] r-modules: fix RVowpalWabbit package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index ed1e276dbbbd..f731e1498e8e 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -336,7 +336,7 @@ let
     rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ];
     rtiff = [ pkgs.libtiff.dev ];
     runjags = [ pkgs.jags ];
-    RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
+    RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
     rzmq = [ pkgs.zeromq3 ];
     SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
     sdcTable = [ pkgs.gmp pkgs.glpk ];

From e1a5eeef06e1b83066ca0645fb2e29e3dbca1f17 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:26:40 +0100
Subject: [PATCH 34/53] r-modules: fix seqinr package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index f731e1498e8e..a2570c8384ff 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -341,7 +341,7 @@ let
     SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
     sdcTable = [ pkgs.gmp pkgs.glpk ];
     seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
-    seqinr = [ pkgs.zlib ];
+    seqinr = [ pkgs.zlib.dev ];
     seqminer = [ pkgs.zlib pkgs.bzip2 ];
     showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
     simplexreg = [ pkgs.gsl_1 ];

From 8a6b58d51d767e043206b3d821e14b4c543ec1d4 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:28:22 +0100
Subject: [PATCH 35/53] r-modules: fix seqminer package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index a2570c8384ff..6a36f9ca7b4f 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -342,7 +342,7 @@ let
     sdcTable = [ pkgs.gmp pkgs.glpk ];
     seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
     seqinr = [ pkgs.zlib.dev ];
-    seqminer = [ pkgs.zlib pkgs.bzip2 ];
+    seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
     showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
     simplexreg = [ pkgs.gsl_1 ];
     SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h

From fcbed4b6549e30a5ac696acd9d068db58ce07451 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:29:12 +0100
Subject: [PATCH 36/53] r-modules: fix showtext package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 6a36f9ca7b4f..5069d67ad723 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -343,7 +343,7 @@ let
     seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
     seqinr = [ pkgs.zlib.dev ];
     seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
-    showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
+    showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
     simplexreg = [ pkgs.gsl_1 ];
     SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
     spate = [ pkgs.fftw ];

From 2303e631165727b94467bd5c1ec16cf8c5c2d3cc Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:30:01 +0100
Subject: [PATCH 37/53] r-modules: fix spate package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 5069d67ad723..be7b7a8143e7 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -346,7 +346,7 @@ let
     showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
     simplexreg = [ pkgs.gsl_1 ];
     SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
-    spate = [ pkgs.fftw ];
+    spate = [ pkgs.fftw.dev ];
     sprint = [ pkgs.openmpi ];
     ssanv = [ pkgs.proj ];
     stsm = [ pkgs.gsl_1 ];

From 9420fa23c65dd5276e7214cff01949e1818504d5 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:31:16 +0100
Subject: [PATCH 38/53] r-modules: fix TAQMNGR package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index be7b7a8143e7..0fcf06b25f57 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -353,7 +353,7 @@ let
     stringi = [ pkgs.icu.dev ];
     survSNP = [ pkgs.gsl_1 ];
     sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
-    TAQMNGR = [ pkgs.zlib ];
+    TAQMNGR = [ pkgs.zlib.dev ];
     tiff = [ pkgs.libtiff ];
     TKF = [ pkgs.gsl_1 ];
     tkrplot = [ pkgs.xorg.libX11 ];

From 0b3e62bb125d6f57dc50b9c0c085e22075a2e1a3 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:32:48 +0100
Subject: [PATCH 39/53] r-modules: fix tiff package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 0fcf06b25f57..140063116078 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -354,7 +354,7 @@ let
     survSNP = [ pkgs.gsl_1 ];
     sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
     TAQMNGR = [ pkgs.zlib.dev ];
-    tiff = [ pkgs.libtiff ];
+    tiff = [ pkgs.libtiff.dev ];
     TKF = [ pkgs.gsl_1 ];
     tkrplot = [ pkgs.xorg.libX11 ];
     topicmodels = [ pkgs.gsl_1 ];

From f9d84f8b65be0aecd17802f13fc7de2845ef26d9 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:37:33 +0100
Subject: [PATCH 40/53] r-modules: fix tkrplot package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 140063116078..3b47fd9f3dec 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -356,7 +356,7 @@ let
     TAQMNGR = [ pkgs.zlib.dev ];
     tiff = [ pkgs.libtiff.dev ];
     TKF = [ pkgs.gsl_1 ];
-    tkrplot = [ pkgs.xorg.libX11 ];
+    tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
     topicmodels = [ pkgs.gsl_1 ];
     udunits2 = [ pkgs.udunits pkgs.expat ];
     V8 = [ pkgs.v8 ];

From 512be9e14ac2f2b37ff7b6ea181cd3854b21acbb Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:39:10 +0100
Subject: [PATCH 41/53] r-modules: fix WhopGenome package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 3b47fd9f3dec..4d12d3ea8b1c 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -362,7 +362,7 @@ let
     V8 = [ pkgs.v8 ];
     VBLPCM = [ pkgs.gsl_1 ];
     VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
-    WhopGenome = [ pkgs.zlib ];
+    WhopGenome = [ pkgs.zlib.dev ];
     XBRL = [ pkgs.zlib pkgs.libxml2 ];
     xml2 = [ pkgs.libxml2 ];
     XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];

From 5b813c2ab0f8469ed76323d6551e67479173e407 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:39:44 +0100
Subject: [PATCH 42/53] r-modules: fix XBRL package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 4d12d3ea8b1c..61b9dd8ba446 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -363,7 +363,7 @@ let
     VBLPCM = [ pkgs.gsl_1 ];
     VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
     WhopGenome = [ pkgs.zlib.dev ];
-    XBRL = [ pkgs.zlib pkgs.libxml2 ];
+    XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
     xml2 = [ pkgs.libxml2 ];
     XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
     affyPLM = [ pkgs.zlib ];

From 1d7fd8f3c4c27e3cece2fb606639a29955b25162 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:40:43 +0100
Subject: [PATCH 43/53] r-modules: fix xml2 package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 61b9dd8ba446..f382a1255014 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -364,7 +364,7 @@ let
     VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
     WhopGenome = [ pkgs.zlib.dev ];
     XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
-    xml2 = [ pkgs.libxml2 ];
+    xml2 = [ pkgs.libxml2.dev ];
     XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
     affyPLM = [ pkgs.zlib ];
     bamsignals = [ pkgs.zlib ];

From c5e4754ca7c7db5b43d7eeb0ccc9cb024120e742 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:42:00 +0100
Subject: [PATCH 44/53] r-modules: fix affyPLM package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index f382a1255014..77453c4e5332 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -366,7 +366,7 @@ let
     XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
     xml2 = [ pkgs.libxml2.dev ];
     XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
-    affyPLM = [ pkgs.zlib ];
+    affyPLM = [ pkgs.zlib.dev ];
     bamsignals = [ pkgs.zlib ];
     BitSeq = [ pkgs.zlib ];
     DiffBind = [ pkgs.zlib ];

From 272b447ea75677ec44843aafabd9c799ebd14ee8 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:43:55 +0100
Subject: [PATCH 45/53] r-modules: fix bamsignals package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 77453c4e5332..a983db5245ef 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -367,7 +367,7 @@ let
     xml2 = [ pkgs.libxml2.dev ];
     XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
     affyPLM = [ pkgs.zlib.dev ];
-    bamsignals = [ pkgs.zlib ];
+    bamsignals = [ pkgs.zlib.dev ];
     BitSeq = [ pkgs.zlib ];
     DiffBind = [ pkgs.zlib ];
     ShortRead = [ pkgs.zlib.dev ];

From 4c0c3c74938e2fb4440059e37f6ab3edae2b1634 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:45:14 +0100
Subject: [PATCH 46/53] r-modules: fix BitSeq package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index a983db5245ef..9275736a377c 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -368,7 +368,7 @@ let
     XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
     affyPLM = [ pkgs.zlib.dev ];
     bamsignals = [ pkgs.zlib.dev ];
-    BitSeq = [ pkgs.zlib ];
+    BitSeq = [ pkgs.zlib.dev ];
     DiffBind = [ pkgs.zlib ];
     ShortRead = [ pkgs.zlib.dev ];
     oligo = [ pkgs.zlib ];

From afd1a4c93366ea2de74f6536874f375ff544e3ee Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:47:08 +0100
Subject: [PATCH 47/53] r-modules: fix affyio package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 9275736a377c..061c930ff834 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -377,7 +377,7 @@ let
     XVector = [ pkgs.zlib.dev ];
     Rsamtools = [ pkgs.zlib.dev ];
     rtracklayer = [ pkgs.zlib ];
-    affyio = [ pkgs.zlib ];
+    affyio = [ pkgs.zlib.dev ];
     VariantAnnotation = [ pkgs.zlib ];
     snpStats = [ pkgs.zlib ];
   };

From 286e86f3a5a9be1fb71e97924667f01e11372557 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:49:49 +0100
Subject: [PATCH 48/53] r-modules: fix oligo package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 061c930ff834..4fd1a1991b5b 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -371,7 +371,7 @@ let
     BitSeq = [ pkgs.zlib.dev ];
     DiffBind = [ pkgs.zlib ];
     ShortRead = [ pkgs.zlib.dev ];
-    oligo = [ pkgs.zlib ];
+    oligo = [ pkgs.zlib.dev ];
     gmapR = [ pkgs.zlib ];
     Rsubread = [ pkgs.zlib ];
     XVector = [ pkgs.zlib.dev ];

From 9ebab25442a1f0bab96d1a39882b8b780e9acf60 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:51:14 +0100
Subject: [PATCH 49/53] r-modules: fix gmapR package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 4fd1a1991b5b..5ce0c0f1344b 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -372,7 +372,7 @@ let
     DiffBind = [ pkgs.zlib ];
     ShortRead = [ pkgs.zlib.dev ];
     oligo = [ pkgs.zlib.dev ];
-    gmapR = [ pkgs.zlib ];
+    gmapR = [ pkgs.zlib.dev ];
     Rsubread = [ pkgs.zlib ];
     XVector = [ pkgs.zlib.dev ];
     Rsamtools = [ pkgs.zlib.dev ];

From baf65d50006138e755f3c53cf1315bed0426533d Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:52:16 +0100
Subject: [PATCH 50/53] r-modules: fix Rsubread package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 5ce0c0f1344b..b1f29791a507 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -373,7 +373,7 @@ let
     ShortRead = [ pkgs.zlib.dev ];
     oligo = [ pkgs.zlib.dev ];
     gmapR = [ pkgs.zlib.dev ];
-    Rsubread = [ pkgs.zlib ];
+    Rsubread = [ pkgs.zlib.dev ];
     XVector = [ pkgs.zlib.dev ];
     Rsamtools = [ pkgs.zlib.dev ];
     rtracklayer = [ pkgs.zlib ];

From 6540b6507dc4d790197240f34141bca82f9dba03 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:53:12 +0100
Subject: [PATCH 51/53] r-modules: fix rtracklayer package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index b1f29791a507..ca59771bd364 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -376,7 +376,7 @@ let
     Rsubread = [ pkgs.zlib.dev ];
     XVector = [ pkgs.zlib.dev ];
     Rsamtools = [ pkgs.zlib.dev ];
-    rtracklayer = [ pkgs.zlib ];
+    rtracklayer = [ pkgs.zlib.dev ];
     affyio = [ pkgs.zlib.dev ];
     VariantAnnotation = [ pkgs.zlib ];
     snpStats = [ pkgs.zlib ];

From b5a0925663fa90a7e8eaa7847e6cce5fc7e87d6f Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:53:49 +0100
Subject: [PATCH 52/53] r-modules: fix VariantAnnotation package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index ca59771bd364..c2c5e24b37fa 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -378,7 +378,7 @@ let
     Rsamtools = [ pkgs.zlib.dev ];
     rtracklayer = [ pkgs.zlib.dev ];
     affyio = [ pkgs.zlib.dev ];
-    VariantAnnotation = [ pkgs.zlib ];
+    VariantAnnotation = [ pkgs.zlib.dev ];
     snpStats = [ pkgs.zlib ];
   };
 

From 8954412fccc04772ac9663fc9c53686f0524a785 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 6 Jan 2017 20:54:40 +0100
Subject: [PATCH 53/53] r-modules: fix snpStats package

---
 pkgs/development/r-modules/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index c2c5e24b37fa..49273e34c7e8 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -379,7 +379,7 @@ let
     rtracklayer = [ pkgs.zlib.dev ];
     affyio = [ pkgs.zlib.dev ];
     VariantAnnotation = [ pkgs.zlib.dev ];
-    snpStats = [ pkgs.zlib ];
+    snpStats = [ pkgs.zlib.dev ];
   };
 
   packagesWithBuildInputs = {