push sheeet

pkgs/development/r-modules/patches/CNEr.patch

@@ -0,0 +1,48 @@
+diff --git a/src/ucsc/common.c b/src/ucsc/common.c
+index a3fc893..e4198d3 100644
+--- a/src/ucsc/common.c
++++ b/src/ucsc/common.c
+@@ -341,7 +341,7 @@ if (count > 1)
+     }
+ }
+ 
+-void slUniqify(void *pList, int (*compare )(const void *elem1,  const void *elem2), void (*free)())
++void slUniqify(void *pList, int (*compare )(const void *elem1,  const void *elem2), void (*freeFunc)())
+ /* Return sorted list with duplicates removed.
+  * Compare should be same type of function as slSort's compare (taking
+  * pointers to pointers to elements.  Free should take a simple
+@@ -356,7 +356,7 @@ while ((el = slPopHead(&oldList)) != NULL)
+     {
+     if ((newList == NULL) || (compare(&newList, &el) != 0))
+         slAddHead(&newList, el);
+-    else if (free != NULL)
++    else if (freeFunc != NULL)
+         free(el);
+     }
+ slReverse(&newList);
+diff --git a/src/ucsc/hash.c b/src/ucsc/hash.c
+index 320b360..6ed9c70 100644
+--- a/src/ucsc/hash.c
++++ b/src/ucsc/hash.c
+@@ -611,7 +611,7 @@ if ((hash = *pHash) != NULL)
+     }
+ }
+ 
+-void hashFreeWithVals(struct hash **pHash, void (freeFunc)())
++void hashFreeWithVals(struct hash **pHash, void (*freeFunc)(void **))
+ /* Free up hash table and all values associated with it. freeFunc is a
+  * function to free an entry, should take a pointer to a pointer to an
+  * entry. */
+diff --git a/src/ucsc/hash.h b/src/ucsc/hash.h
+index a7fc017..0d06bb9 100644
+--- a/src/ucsc/hash.h
++++ b/src/ucsc/hash.h
+@@ -244,7 +244,7 @@ void freeHashAndVals(struct hash **pHash);
+ /* Free up hash table and all values associated with it.
+  * (Just calls freeMem on each hel->val) */
+ 
+-void hashFreeWithVals(struct hash **pHash, void (freeFunc)());
++void hashFreeWithVals(struct hash **pHash, void (*freeFunc)(void **));
+ /* Free up hash table and all values associated with it. freeFunc is a
+  * function to free an entry, should take a pointer to a pointer to an
+  * entry. */

pkgs/development/r-modules/patches/FLAMES.patch

@@ -0,0 +1,17 @@
+diff --git a/src/Makevars b/src/Makevars
+index 4f3fa42ce752..e48e45561292 100755
+--- a/src/Makevars
++++ b/src/Makevars
+@@ -24,12 +24,6 @@ FILES = $(CFILES) $(CPPFILES)
+ SOURCES = $(FILES)
+ OBJECTS = $(CPPFILES:.cpp=.o) $(CFILES:.c=.o)
+ 
+-strippedLib: $(SHLIB)
+-	if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug $(SHLIB); fi
+-clean:
+-	rm $(OBJECTS)
+-.phony: strippedLib clean
+-
+ RHTSLIB_LIBS=$(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e \
+     'Rhtslib::pkgconfig("PKG_LIBS")')
+ RHTSLIB_CPPFLAGS=$(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e \

pkgs/development/r-modules/patches/RAppArmor.patch

@@ -0,0 +1,20 @@
+diff -ru -x '*~' RAppArmor_orig/configure RAppArmor/configure
+--- RAppArmor_orig/configure	2013-12-17 11:23:00.000000000 +0900
++++ RAppArmor/configure	2014-10-18 22:22:39.641341244 +0900
+@@ -1,15 +1,2 @@
+-if [ ! -e /usr/include/sys/apparmor.h ]
+-then
+-  echo "sys/apparmor.h not found. Make sure libapparmor-dev is installed."
+-  exit 1
+-fi
+-
+-LIBFILE=$(/sbin/ldconfig -p | egrep -oh " [-_a-zA-Z0-9/]*/libapparmor.so(.1)?$")
+-
+-if [ -z "$LIBFILE" ]
+-then
+-  echo "libapparmor.so not found. Make sure libapparmor-dev is installed."
+-  exit 1
+-fi 
+-
++LIBFILE="$LIBAPPARMOR_HOME/lib/libapparmor.so.1"
+ echo "PKG_LIBS="$LIBFILE > src/Makevars

pkgs/development/r-modules/patches/Rhdf5lib.patch

@@ -0,0 +1,79 @@
+diff --git a/R/zzz.R b/R/zzz.R
+index 97becd7..803ca39 100644
+--- a/R/zzz.R
++++ b/R/zzz.R
+@@ -20,7 +20,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+ 
+   path <- Sys.getenv(
+     x = "RHDF5LIB_RPATH",
+-    unset = system.file("lib", package="Rhdf5lib", mustWork=TRUE)
++    unset = ""
+   )
+ 
+   if (nzchar(.Platform$r_arch)) {
+@@ -59,7 +59,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5 %s',
+                                       patharch, winlibs)
+                             }, {
+-                              sprintf('"%s/libhdf5.a"%s%s', 
++                              sprintf('-lhdf5',
+                                       patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                             }
+                      )
+@@ -70,7 +70,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5_cpp -lhdf5 %s',
+                                       patharch, winlibs)
+                             }, {
+-                              sprintf('"%s/libhdf5_cpp.a" "%s/libhdf5.a"%s%s',
++                              sprintf('-lhdf5_cpp -lhdf5',
+                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                             }
+                      )
+@@ -81,7 +81,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5_hl -lhdf5 %s',
+                                       patharch, winlibs)
+                             }, {
+-                              sprintf('"%s/libhdf5_hl.a" "%s/libhdf5.a"%s%s', 
++                              sprintf('-lhdf5_hl -lhdf5',
+                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                             }
+                      )
+@@ -92,7 +92,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 %s',
+                                       patharch, winlibs)
+                             }, {
+-                              sprintf('"%s/libhdf5_hl_cpp.a" "%s/libhdf5_hl.a" "%s/libhdf5_cpp.a" "%s/libhdf5.a"%s%s',
++                              sprintf('-lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5',
+                                       patharch, patharch, patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                             }
+                      )
+@@ -124,6 +124,7 @@ getHdf5Version <- function() {
+ #'
+ #' @keywords internal
+ .getDynamicLinks <- function() {
++  return("")
+   sysname <- Sys.info()['sysname']
+   if(sysname == "Windows") {
+     links <- "-lz"
+diff --git a/src/Makevars.in b/src/Makevars.in
+index addb6a0..590784a 100644
+--- a/src/Makevars.in
++++ b/src/Makevars.in
+@@ -18,7 +18,7 @@ USER_LIB_DIR = ${R_PACKAGE_DIR}/lib${R_ARCH}/
+ 
+ PKG_CPPFLAGS = -I${USER_INCLUDE_DIR} ${ZLIB_INCLUDE}
+ PKG_CFLAGS = ${ZLIB_LIB}
+-PKG_LIBS = "${USER_LIB_DIR}libhdf5.a" @SZIP_LIB@ -lz
++PKG_LIBS = -lhdf5 -lsz
+ 
+ 
+ 
+@@ -26,7 +26,7 @@ all: $(SHLIB)
+ 
+ $(SHLIB): Rhdf5lib.o
+ 
+-Rhdf5lib.o: copy-hdf5 @COPY_SZIP@
++Rhdf5lib.o:
+ 
+ copy-szip: copy-hdf5
+ 	cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "${USER_LIB_DIR}"

pkgs/development/r-modules/patches/Rserve.patch

@@ -0,0 +1,15 @@
+diff -ru -x '*~' Rserve_orig/src/Makevars.in Rserve/src/Makevars.in
+--- Rserve_orig/src/Makevars.in	2013-08-22 06:09:33.000000000 +0900
++++ Rserve/src/Makevars.in	2014-11-09 21:36:31.184590320 +0900
+@@ -12,8 +12,9 @@
+ 	$(CC) -DSTANDALONE_RSERVE -DRSERV_DEBUG -DNODAEMON -I. -Iinclude $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(PKG_CPPFLAGS) $(PKG_CFLAGS) -o Rserve.dbg $(SERVER_SRC) $(ALL_LIBS) $(PKG_LIBS)
+ 
+ # merging to bin/Rserve works only if installed from sources, won't work for binary
+-	-./mergefat Rserve "$(R_HOME)/bin/Rserve"
+-	-./mergefat Rserve.dbg "$(R_HOME)/bin/Rserve.dbg"
++	mkdir $(out)/bin
++	-./mergefat Rserve "$(out)/bin/Rserve"
++	-./mergefat Rserve.dbg "$(out)/bin/Rserve.dbg"
+ 
+ client: config.h
+ 	cp config.h client/cxx/

pkgs/development/r-modules/patches/immunotation.patch

@@ -0,0 +1,47 @@
+diff --git a/R/AFND_interface.R b/R/AFND_interface.R
+index b62e8e0..0f22d85 100644
+--- a/R/AFND_interface.R
++++ b/R/AFND_interface.R
+@@ -244,9 +244,9 @@ check_population <- function(hla_population) {
+ #' @return list of valid countries, regions and ethnic origin
+ #' @keywords internal
+ get_valid_geographics <- function() {
+-    url <- "http://www.allelefrequencies.net/hla6006a.asp?"
+-    html_input <- getURL(url, read_method = "html")
+-    
++    # http://www.allelefrequencies.net/hla6006a.asp?
++    html_input <- xml2::read_html("nix-valid-geographics")
++      
+     rvest_tables <- rvest::html_table(html_input, fill = TRUE)
+     
+     # country
+diff --git a/R/external_resources_input.R b/R/external_resources_input.R
+index c4b1dc1..8fc5881 100644
+--- a/R/external_resources_input.R
++++ b/R/external_resources_input.R
+@@ -74,16 +74,17 @@ getURL <- function(URL, N.TRIES=2L,
+ # MHC I
+ # netmhcI_input_template is an internal variable containing list of valid 
+ # NetMHCpan input alleles
+-netmhcI_input_template <- getURL(
+-    URL="https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list",
+-    read_method = "delim", delim = "\t",
+-    col_names = c("netmhc_input", "hla_chain_name", "HLA_gene"))
++netmhcI_input_template <- readr::read_delim(
++        # https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list
++	"nix-NetMHCpan-4.1-allele-list",
++	delim = "\t",
++	skip = 0,
++        col_names = c("netmhc_input", "hla_chain_name", "HLA_gene")
++    )
+ 
+ # MHC II
+-lines <- getURL(
+-    URL = paste0("https://services.healthtech.dtu.dk/services/",
+-    "NetMHCIIpan-4.0/alleles_name.list"),
+-    read_method = "lines")
++# https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list
++lines <- readr::read_lines("nix-NETMHCIIpan-4.0-alleles-name-list")
+ lines_rep <- stringr::str_replace_all(lines, "\t+|\\s\\s+", "\t")
+ netmhcII_input_template <- suppressWarnings(
+     suppressMessages(read.delim(textConnection(lines_rep), sep = "\t")))

pkgs/development/r-modules/patches/rhdf5.patch

@@ -0,0 +1,47 @@
+diff --git a/src/Makevars b/src/Makevars
+index 713b44c..704ac17 100644
+--- a/src/Makevars
++++ b/src/Makevars
+@@ -1,5 +1,5 @@
+ RHDF5_LIBS = $(shell "$(R_HOME)/bin${R_ARCH_BIN}/Rscript" -e 'Rhdf5lib::pkgconfig("PKG_C_LIBS")')
+-PKG_LIBS = $(RHDF5_LIBS)
++PKG_LIBS = $(RHDF5_LIBS) -lhdf5
+ 
+ #PKG_CFLAGS = -Wall
+ 
+diff --git a/src/h5testLock.c b/src/h5testLock.c
+index b326444..5d58b4a 100644
+--- a/src/h5testLock.c
++++ b/src/h5testLock.c
+@@ -8,16 +8,16 @@ SEXP _h5fileLock(SEXP _file_name) {
+   int lk = -1;
+ 
+   /* create the temporary file */
+-  fd = HDopen(file_name, O_RDWR | O_CREAT | O_TRUNC, 0666);
++  fd = open(file_name, O_RDWR | O_CREAT | O_TRUNC, 0666);
+ 
+   /* try to lock file */
+-  lk = HDflock(fd, LOCK_EX | LOCK_NB);
++  lk = flock(fd, LOCK_EX | LOCK_NB);
+   
+   /* unlock so we can remove */
+-  HDflock(fd, LOCK_UN);
++  flock(fd, LOCK_UN);
+   
+   /* close */
+-  HDclose(fd);
++  close(fd);
+   
+   /* return value of lock attempt */
+   PROTECT(Rval = allocVector(INTSXP, 1));
+diff --git a/src/h5testLock.h b/src/h5testLock.h
+index 2c1c5e4..25914ff 100644
+--- a/src/h5testLock.h
++++ b/src/h5testLock.h
+@@ -1,5 +1,5 @@
+ #include <fcntl.h>
++#include <unistd.h>
+ #include "myhdf5.h"
+-#include <H5private.h>
+ 
+ SEXP _h5fileLock();

pkgs/development/r-modules/patches/rhdf5filters.patch

@@ -0,0 +1,12 @@
+diff --git a/src/Makevars.in b/src/Makevars.in
+--- a/src/Makevars.in
++++ b/src/Makevars.in
+@@ -15,7 +15,7 @@ RANLIB := @RANLIB@
+ MAKE := @MAKE@
+ AR := @AR@
+-PKG_CPPFLAGS := @CPPFLAGS@ -I"@RHDF5_INCLUDE@"
++PKG_CPPFLAGS := @CPPFLAGS@
+ PKG_LDFLAGS := @LDFLAGS@
+ export
+
+ all: copying $(SHLIB)

pkgs/development/r-modules/patches/universalmotif.patch

@@ -0,0 +1,10 @@
+diff --git a/src/Makevars b/src/Makevars
+index 6e08950..e66fbbd 100644
+--- a/src/Makevars
++++ b/src/Makevars
+@@ -1,5 +1 @@
+ CXX_STD=CXX11
+-PKG_LIBS=`"$(R_HOME)/bin/Rscript" -e "RcppThread::LdFlags()"`
+-strippedLib: $(SHLIB)
+-		if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug $(SHLIB); fi
+-.phony: strippedLib