pkg/26650: pkgsrc/biology/hmmer does not honor $MKDIR

[geos%epost.de@localhost]

>Number:         26650
>Category:       pkg
>Synopsis:       pkgsrc/biology/hmmer does not honor $MKDIR
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    pkg-manager
>State:          open
>Class:          sw-bug
>Submitter-Id:   net
>Arrival-Date:   Sat Aug 14 13:23:00 UTC 2004
>Closed-Date:
>Last-Modified:
>Originator:     Georg Schwarz
>Release:        current pkgsrc
>Organization:
>Environment:
IRIX lorenz 5.3 08031225 IP20 mips
>Description:
pkgsrc/biology/hmmer uses mkdir -p instead of ${MKDIR} for installation, which 
on some platforms fails when trying to create an already existing directory.
>How-To-Repeat:

>Fix:
patch Makefile.in (or rather change the respective patch):

--- Makefile.in.orig    Sat Aug 14 14:13:37 2004
+++ Makefile.in Sat Aug 14 14:14:39 2004
@@ -110,8 +110,8 @@
 #          installs man pages in MANDIR/man1/  (e.g. if MANSUFFIX is 1)
 #          Creates these directories if they don't exist.
 install: 
-       mkdir -p ${BINDIR}
-       -mkdir -p ${MANDIR}/man${MANSUFFIX}
+       ${MKDIR} ${BINDIR}
+       -${MKDIR} ${MANDIR}/man${MANSUFFIX}
        for file in $(PROGS) $(PVMPROGS); do\
           $(INSTBIN) src/$$file $(BINDIR)/;\
        done
@@ -134,7 +134,7 @@
 #          subdir, remove everything but binaries and Makefiles.
 #
 bindist:
-       mkdir binaries
+       ${MKDIR} binaries
        for prog in $(PROGS); do\
           (cd binaries; ln -s ../src/$$prog .);\
        done
@@ -206,7 +206,7 @@
        # in testsuite. 
        #
        cp ssdk/sqc ${BASENAME}-${RELEASE}/testsuite/
-       mkdir ${BASENAME}-${RELEASE}/ssdk
+       ${MKDIR} ${BASENAME}-${RELEASE}/ssdk
        cp ssdk/rmanprocess.pl ${BASENAME}-${RELEASE}/ssdk/
        # 
        # Make the configure scripts from configure.ac
@@ -294,7 +294,7 @@
 #               directory.
 #
 ftpdist:
-       mkdir -p ${FTPDIR}
+       ${MKDIR} ${FTPDIR}
        cp -f hmmer-$(RELEASE)/00README         ${FTPDIR}
        cp -f hmmer-$(RELEASE)/COPYRIGHT        ${FTPDIR}
        cp -f hmmer-$(RELEASE)/INSTALL          ${FTPDIR}


Moreover, it seems necessary to add the following to the toplevel Makefile:

MAKE_FLAGS+=            MKDIR="${MKDIR}"
>Release-Note:
>Audit-Trail:
>Unformatted: