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Bug 380397 - sci-misc/h5utils-1.12.1 USE=octave - ACCESS DENIED: unlink: /usr/libexec/octave/3.2.4/site/oct/x86_64-pc-linux-gnu/h5read.oct
Summary: sci-misc/h5utils-1.12.1 USE=octave - ACCESS DENIED: unlink: /usr/libexe...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2011-08-23 17:05 UTC by Ruggero Morsucci
Modified: 2011-08-25 15:58 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


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Description Ruggero Morsucci 2011-08-23 17:05:59 UTC
>>> Install h5utils-1.12.1 into /var/tmp/portage/sci-misc/h5utils-1.12.1/image/ category sci-misc
x86_64-pc-linux-gnu-gcc  -march=nocona -O3 -pipe  -Wl,-O1 -Wl,--as-needed -o h5totxt h5totxt.o arrayh5.o h5utils.o  -lhdf5 -lz -lm 
x86_64-pc-linux-gnu-gcc  -march=nocona -O3 -pipe  -Wl,-O1 -Wl,--as-needed -o h5fromtxt h5fromtxt.o arrayh5.o h5utils.o  -lhdf5 -lz -lm 
x86_64-pc-linux-gnu-gcc  -march=nocona -O3 -pipe  -Wl,-O1 -Wl,--as-needed -o h5tovtk h5tovtk.o arrayh5.o h5utils.o  -lhdf5 -lz -lm 
x86_64-pc-linux-gnu-gcc  -march=nocona -O3 -pipe  -Wl,-O1 -Wl,--as-needed -o h5topng h5topng.o writepng.o arrayh5.o h5utils.o -lpng -lhdf5 -lz -lm 
x86_64-pc-linux-gnu-gcc  -march=nocona -O3 -pipe  -Wl,-O1 -Wl,--as-needed -o h5fromitxt h5fromitxt.o arrayh5.o h5utils.o  -lhdf5 -lz -lm 
make[1]: Entering directory `/var/tmp/portage/sci-misc/h5utils-1.12.1/work/h5utils-1.12.1'
test -z "/var/tmp/portage/sci-misc/h5utils-1.12.1/image/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-misc/h5utils-1.12.1/image/usr/bin"
  /usr/bin/install -c h5totxt h5fromtxt h5tovtk h5topng '/var/tmp/portage/sci-misc/h5utils-1.12.1/image/usr/bin'
test -z "/var/tmp/portage/sci-misc/h5utils-1.12.1/image/usr/share/man/man1" || /bin/mkdir -p "/var/tmp/portage/sci-misc/h5utils-1.12.1/image/usr/share/man/man1"
 /usr/bin/install -c -m 644 h5totxt.1 h5fromtxt.1 h5tovtk.1 h5topng.1 '/var/tmp/portage/sci-misc/h5utils-1.12.1/image/usr/share/man/man1'
test -z "/var/tmp/portage/sci-misc/h5utils-1.12.1/image/usr/share/h5utils" || /bin/mkdir -p "/var/tmp/portage/sci-misc/h5utils-1.12.1/image/usr/share/h5utils"
/bin/mkdir -p '/var/tmp/portage/sci-misc/h5utils-1.12.1/image/usr/share/h5utils/colormaps'
 /usr/bin/install -c -m 644  colormaps/autumn colormaps/bluered colormaps/bone colormaps/colorcube colormaps/cool colormaps/copper colormaps/flag colormaps/gray colormaps/green colormaps/hot colormaps/hsv colormaps/jet colormaps/lines colormaps/pink colormaps/prism colormaps/spring colormaps/summer colormaps/vga colormaps/winter colormaps/yarg colormaps/yellow colormaps/dkbluered '/var/tmp/portage/sci-misc/h5utils-1.12.1/image/usr/share/h5utils/colormaps'
test -z "/usr/libexec/octave/3.2.4/site/oct/x86_64-pc-linux-gnu" || /bin/mkdir -p "/usr/libexec/octave/3.2.4/site/oct/x86_64-pc-linux-gnu"
 /usr/bin/install -c -m 644 h5read.oct '/usr/libexec/octave/3.2.4/site/oct/x86_64-pc-linux-gnu'
[31;01mACCESS DENIED[0m  unlink:       /usr/libexec/octave/3.2.4/site/oct/x86_64-pc-linux-gnu/h5read.oct
/usr/bin/install: cannot remove `/usr/libexec/octave/3.2.4/site/oct/x86_64-pc-linux-gnu/h5read.oct': Permission denied
make[1]: *** [install-octDATA] Error 1
make[1]: Leaving directory `/var/tmp/portage/sci-misc/h5utils-1.12.1/work/h5utils-1.12.1'
make: *** [install-am] Error 2
 [31;01m*[0m ERROR: sci-misc/h5utils-1.12.1 failed (install phase):
 [31;01m*[0m   einstall failed
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line   56:  Called src_install
 [31;01m*[0m   environment, line 2716:  Called einstall
 [31;01m*[0m     ebuild.sh, line  602:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   		${MAKE:-make} prefix="${D}usr" \
 [31;01m*[0m   			datadir="${D}usr/share" \
 [31;01m*[0m   			infodir="${D}usr/share/info" \
 [31;01m*[0m   			localstatedir="${D}var/lib" \
 [31;01m*[0m   			mandir="${D}usr/share/man" \
 [31;01m*[0m   			sysconfdir="${D}etc" \
 [31;01m*[0m   			${LOCAL_EXTRA_EINSTALL} \
 [31;01m*[0m   			${MAKEOPTS} ${EXTRA_EMAKE} -j1 \
 [31;01m*[0m   			"$@" install || die "einstall failed"
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of 'emerge --info =sci-misc/h5utils-1.12.1',
 [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-misc/h5utils-1.12.1'.
 [31;01m*[0m This ebuild is from an overlay named 'fix': '/usr/local/portage/fix/'
 [31;01m*[0m The complete build log is located at '/var/log/portage/sci-misc:h5utils-1.12.1:20110719-155514.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-misc/h5utils-1.12.1/temp/environment'.
 [31;01m*[0m S: '/var/tmp/portage/sci-misc/h5utils-1.12.1/work/h5utils-1.12.1'
[31;01m--------------------------- ACCESS VIOLATION SUMMARY ---------------------------[0m
[31;01mLOG FILE[0m "/var/log/sandbox/sandbox-29634.log"

VERSION 1.0
FORMAT: F - Function called
FORMAT: S - Access Status
FORMAT: P - Path as passed to function
FORMAT: A - Absolute Path (not canonical)
FORMAT: R - Canonical Path
FORMAT: C - Command Line

F: unlink
S: deny
P: /usr/libexec/octave/3.2.4/site/oct/x86_64-pc-linux-gnu/h5read.oct
A: /usr/libexec/octave/3.2.4/site/oct/x86_64-pc-linux-gnu/h5read.oct
R: /usr/libexec/octave/3.2.4/site/oct/x86_64-pc-linux-gnu/h5read.oct
C: /usr/bin/install -c -m 644 h5read.oct /usr/libexec/octave/3.2.4/site/oct/x86_64-pc-linux-gnu 
[31;01m--------------------------------------------------------------------------------[0m


This fix the issue for me:

--- /usr/portage/sci-misc/h5utils/h5utils-1.12.1.ebuild.old 2009-08-04 07:53:45.000000000 +0200
+++ /usr/portage/sci-misc/h5utils/h5utils-1.12.1.ebuild.new 2009-08-04 07:53:45.000000000 +0200
@@ -22,6 +24,6 @@
 }

 src_install() {
-       einstall || die
+       emake DESTDIR="${D}" install || die
        dodoc README NEWS AUTHORS
 }

Error:


Reproducible: Always
Comment 1 Jeroen Roovers (RETIRED) gentoo-dev 2011-08-25 14:26:16 UTC
Oh it should definitely drop einstall.
Comment 2 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2011-08-25 15:58:01 UTC
+*h5utils-1.12.1-r1 (25 Aug 2011)
+
+  25 Aug 2011; Kacper Kowalik <xarthisius@gentoo.org>
+  -files/1.10-octave-path.patch, -h5utils-1.10.ebuild, -h5utils-1.12.1.ebuild,
+  +h5utils-1.12.1-r1.ebuild:
+  Update ebuild to fix sandbox violation during install phase. Fixes bug 380397
+  by Ruggero Morsucci <morse@supercomputing.univpm.it>. Drop old