internlm/SWE-Fixer-Train-110K huggingface dataset:
Repository: spack/spack

Issue:
installation of clapack fails

Trying to install clapack with spack, I get the following error:

### Expected Result

clapack to be installed

### Actual Result

```console
$ spack install clapack@3.2.1%gcc@5.4.0
==> atlas is already installed in /astro/soft/common/spack/v20180409/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/atlas-3.10.2-yp5nvd2ochyl26dssffadntiix5pyiaf
==> Installing clapack
==> Using cached archive: /astro/soft/common/spack/v20180409/spack/var/spack/cache/clapack/clapack-3.2.1.tgz
==> Staging archive: /astro/soft/common/spack/v20180409/spack/var/spack/stage/clapack-3.2.1-4n66tr3jf4vwl53yr3lz7ptw7jspqqd4/clapack.tgz
==> Created stage in /astro/soft/common/spack/v20180409/spack/var/spack/stage/clapack-3.2.1-4n66tr3jf4vwl53yr3lz7ptw7jspqqd4
==> No patches needed for clapack
==> Building clapack [MakefilePackage]
==> Executing phase: 'edit'
==> Error: NameError: global name 'makefile' is not defined

/astro/soft/common/spack/v20180409/spack/var/spack/repos/builtin/packages/clapack/package.py:53, in edit:
         50            make_inc = FileFilter('make.inc')
         51            make_inc.filter(r'^BLASLIB.*',
         52                            'BLASLIB = ../../libcblaswr.a -lcblas -latlas')
  >>     53            makefile.filter(r'^lib.*',
         54                            'lib: variants lapacklib tmglib')

```


### Information on your system

- Done in centos 7
- spack up to date


Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/clapack/package.py b/var/spack/repos/builtin/packages/clapack/package.py
--- a/var/spack/repos/builtin/packages/clapack/package.py
+++ b/var/spack/repos/builtin/packages/clapack/package.py
@@ -50,6 +50,7 @@ def edit(self, spec, prefix):
             make_inc = FileFilter('make.inc')
             make_inc.filter(r'^BLASLIB.*',
                             'BLASLIB = ../../libcblaswr.a -lcblas -latlas')
+            makefile = FileFilter('Makefile')
             makefile.filter(r'^lib.*',
                             'lib: variants lapacklib tmglib')
 


Test patch:
Repository: spack/spack

Issue:
Installation issue: gcc@8.,3.0 with centos7 default compiler
### Steps to reproduce the issue

```console
$ spack install gcc@8.3.0
...
  >> 2426    checking for off_t... checking size of long long... configure: err
             or: in `spack-stage-gcc-8.3.0-6ypg
             gmswzvrzgw3lq6tovkv23mect6ee/spack-src/spack-build/gcc':
  >> 2427    configure: error: cannot compute sizeof (long long)
```

### Information on your system

$ spack debug report
* **Spack:** 0.15.0
* **Python:** 3.6.8
* **Platform:** linux-centos7-broadwell

### Additional information

Related to #3943 and #1866 which were not properly fixed but *avoided*.

PR #9024 solves this issue. (and I think +binutils should become the default).

Maintainer is @michaelkuhn .

### General information

<!-- These boxes can be checked by replacing [ ] with [x] or by clicking them after submitting the issue. -->
- [x] I have run `spack debug report` and reported the version of Spack/Python/Platform
- [x] I have run `spack maintainers <name-of-the-package>` and @mentioned any maintainers
- [ ] I have uploaded the build log and environment files
- [x] I have searched the issues of this repo and believe this is not a duplicate



Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -115,7 +115,7 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
     depends_on('zstd', when='@10:')
     depends_on('iconv', when='platform=darwin')
     depends_on('gnat', when='languages=ada')
-    depends_on('binutils~libiberty', when='+binutils')
+    depends_on('binutils~libiberty', when='+binutils', type=('build', 'link', 'run'))
     depends_on('zip', type='build', when='languages=java')
     depends_on('cuda', when='+nvptx')
 
@@ -373,8 +373,6 @@ def configure_args(self):
         # enable appropriate bootstrapping flags
         stage1_ldflags = str(self.rpath_args)
         boot_ldflags = stage1_ldflags + ' -static-libstdc++ -static-libgcc'
-        if '%gcc' in spec:
-            stage1_ldflags = boot_ldflags
         options.append('--with-stage1-ldflags=' + stage1_ldflags)
         options.append('--with-boot-ldflags=' + boot_ldflags)
 


Test patch:
Repository: spack/spack

Issue:
MVAPICH2 depends on libibverbs
I was testing out Spack by attempting an installation of mvapich2 on my Fedora laptop. Of course, I don't have any libibverbs installed on my laptop, and even with all of the variants disabled, I was unable to build mvapich2:
```
configure: error: 'libibverbs not found. Did you specify --with-ib-libpath=?'
```
I could use the system package manager to do this, but how would people feel about a Spack package for libibverbs? It looks like you can download it here:
https://www.openfabrics.org/downloads/libibverbs/


Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -121,6 +121,10 @@ class Mvapich2(AutotoolsPackage):
     depends_on('libpciaccess', when=(sys.platform != 'darwin'))
     depends_on('cuda', when='+cuda')
     depends_on('psm', when='fabrics=psm')
+    depends_on('rdma-core', when='fabrics=mrail')
+    depends_on('rdma-core', when='fabrics=nemesisib')
+    depends_on('rdma-core', when='fabrics=nemesistcpib')
+    depends_on('rdma-core', when='fabrics=nemesisibtcp')
 
     filter_compiler_wrappers(
         'mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpifort', relative_root='bin'
@@ -180,7 +184,8 @@ def network_options(self):
         elif 'fabrics=nemesis' in self.spec:
             opts = ["--with-device=ch3:nemesis"]
         elif 'fabrics=mrail' in self.spec:
-            opts = ["--with-device=ch3:mrail", "--with-rdma=gen2"]
+            opts = ["--with-device=ch3:mrail", "--with-rdma=gen2",
+                    "--disable-mcast"]
         return opts
 
     @property


Test patch:
Repository: spack/spack

Issue:
Installation issue: atk failes due to python version mismatch
### Steps to reproduce the issue

```console
$ spack spec atk
Input spec
--------------------------------
atk

Concretized
--------------------------------
==> Error: An unsatisfiable version constraint has been detected for spec:

    python@2.7.15%gcc@7.3.0+dbm~optimizations+pic+pythoncmd+shared~tk~ucs4 arch=linux-ubuntu16.04-x86_64 
        ^bzip2@1.0.6%gcc@7.3.0+shared arch=linux-ubuntu16.04-x86_64 
        ^gdbm@1.14.1%gcc@7.3.0 arch=linux-ubuntu16.04-x86_64 
            ^readline@7.0%gcc@7.3.0 arch=linux-ubuntu16.04-x86_64 
                ^ncurses@6.1%gcc@7.3.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64 
                    ^pkgconf@1.4.2%gcc@7.3.0 arch=linux-ubuntu16.04-x86_64 
        ^openssl@1.0.2o%gcc@7.3.0+systemcerts arch=linux-ubuntu16.04-x86_64 
            ^zlib@1.2.11%gcc@7.3.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 
        ^sqlite@3.23.1%gcc@7.3.0~functions arch=linux-ubuntu16.04-x86_64 


while trying to concretize the partial spec:

    meson


meson requires python version 3:, but spec asked for 2.7.15
```

### Platform and user environment

Please report your OS here:
```commandline
$ uname -a 
Linux west1 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
$ lsb_release -d
Description:    Ubuntu 16.04.4 LTS
``` 
### Additional information

The problem is that atk depends on glib (which depends on python2 by default) and in the most current version on meson, which requires python3



Discussion:
I can concretize at least if I provide a newer python version as a hint: `spack spec atk ^python@3.6.5` - does that work for you here?
Works for me, should be default behaviour for current atk version

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/atk/package.py b/var/spack/repos/builtin/packages/atk/package.py
--- a/var/spack/repos/builtin/packages/atk/package.py
+++ b/var/spack/repos/builtin/packages/atk/package.py
@@ -41,6 +41,12 @@ class Atk(Package):
 
     depends_on('meson', type='build', when='@2.28.0:')
     depends_on('glib')
+    # FIXME: this constraint exists because of the meson dependency.
+    # It should not be required to specify it here, but "spack spec atk" will
+    # fail without it.
+    # See: #2632
+    depends_on('python@3:')
+    depends_on('gettext')
     depends_on('pkgconfig', type='build')
     depends_on('gobject-introspection')
 


Test patch:
Repository: spack/spack

Issue:
py-matplotlib: Add patch to fix FreeType library detection
Adds patch to add $CPATH to locations searched for FreeType header file

Patch has been upstreamed:
https://github.com/matplotlib/matplotlib/pull/11457


Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py
--- a/var/spack/repos/builtin/packages/py-matplotlib/package.py
+++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py
@@ -34,6 +34,7 @@ class PyMatplotlib(PythonPackage):
     homepage = "https://pypi.python.org/pypi/matplotlib"
     url      = "https://pypi.io/packages/source/m/matplotlib/matplotlib-2.0.2.tar.gz"
 
+    version('2.2.3', '403b0bddd751d71187416f20d4cff100')
     version('2.2.2', 'dd1e49e041309a7fd4e32be8bf17c3b6')
     version('2.0.2', '061111784278bde89b5d4987014be4ca')
     version('2.0.0', '7aa54b06327f0e1c4f3877fc2f7d6b17')
@@ -68,6 +69,7 @@ class PyMatplotlib(PythonPackage):
 
     depends_on('libpng@1.2:')
     depends_on('freetype@2.3:')
+    patch('freetype-include-path.patch', when='@2.2.2:2.9.9')  # Patch to pick up correct freetype headers
 
     depends_on('py-numpy@1.6:', type=('build', 'run'))
     depends_on('py-dateutil@1.1:', type=('build', 'run'))


Test patch:
Repository: spack/spack

Issue:
cistem - fixed url which does not work



Discussion:
This PR doesn't actually fix anything, it just makes it so that you can only manually download the URL.

It looks like there is a problem in our version parsing. Let me submit a fix for that.

Resolving patch:
diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py
--- a/lib/spack/spack/url.py
+++ b/lib/spack/spack/url.py
@@ -169,6 +169,7 @@ def strip_version_suffixes(path):
         # Download type
         '[Ii]nstall',
         'all',
+        'code',
         'src(_0)?',
         '[Ss]ources?',
         'file',
diff --git a/var/spack/repos/builtin/packages/cistem/package.py b/var/spack/repos/builtin/packages/cistem/package.py
--- a/var/spack/repos/builtin/packages/cistem/package.py
+++ b/var/spack/repos/builtin/packages/cistem/package.py
@@ -34,7 +34,7 @@ class Cistem(AutotoolsPackage):
     homepage = "https://cistem.org/"
     url      = "https://cistem.org/system/tdf/upload3/cistem-1.0.0-beta-source-code.tar.gz?file=1&type=cistem_details&id=37&force=0"
 
-    version('1.0.0', '479f395b30ad630df3cbba9c56eb29c2')
+    version('1.0.0-beta', '479f395b30ad630df3cbba9c56eb29c2')
 
     depends_on('wx@3.0.2')
     depends_on('fftw')


Test patch:
diff --git a/lib/spack/spack/test/url_parse.py b/lib/spack/spack/test/url_parse.py
--- a/lib/spack/spack/test/url_parse.py
+++ b/lib/spack/spack/test/url_parse.py
@@ -43,6 +43,8 @@
     ('jpegsrc.v9b', 'jpegsrc.v9b'),
     ('turbolinux702', 'turbolinux702'),
     ('converge_install_2.3.16', 'converge_install_2.3.16'),
+    # Download type - code, source
+    ('cistem-1.0.0-beta-source-code', 'cistem-1.0.0-beta'),
     # Download type - src
     ('apache-ant-1.9.7-src', 'apache-ant-1.9.7'),
     ('go1.7.4.src', 'go1.7.4'),
Repository: spack/spack

Issue:
VTK package fails with AttributeError: 'Gcc' object has no attribute 'is_apple'
### Steps to reproduce the issue

```console
$ spack install vtk
```

### Error Message

```
==> Error: AttributeError: 'Gcc' object has no attribute 'is_apple'

/home/mdorier/spack/var/spack/repos/builtin/packages/vtk/package.py:215, in cmake_args:
        212            # string. This fix was recommended on the VTK mailing list
        213            # in March 2014 (see
        214            # https://public.kitware.com/pipermail/vtkusers/2014-March/083368.html)
  >>    215            if (self.compiler.is_apple and
        216                self.compiler.version >= Version('5.1.0')):
        217                cmake_args.extend(['-DVTK_REQUIRED_OBJCXX_FLAGS=""'])
        218
```


Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py
--- a/var/spack/repos/builtin/packages/vtk/package.py
+++ b/var/spack/repos/builtin/packages/vtk/package.py
@@ -212,7 +212,8 @@ def cmake_args(self):
             # string. This fix was recommended on the VTK mailing list
             # in March 2014 (see
             # https://public.kitware.com/pipermail/vtkusers/2014-March/083368.html)
-            if (self.compiler.is_apple and
+            if (self.spec.satisfies('%clang') and
+                self.compiler.is_apple and
                 self.compiler.version >= Version('5.1.0')):
                 cmake_args.extend(['-DVTK_REQUIRED_OBJCXX_FLAGS=""'])
 


Test patch:
Repository: spack/spack

Issue:
Installation issue: font-adobe-75dpi on linux-centos7-ppc64le

On our Power cluster, linux-centos7-ppc64le 
current font-adobe-75dpi configure complain of old ./config.guess too old and not able to 
decide build type

### Steps to reproduce the issue

```console
$ spack install font-adobe-75dpi


==> Executing phase: 'install'
==> Error: ProcessError: Command exited with status 1:
    './configure' '--prefix=/davide_scratch/userinternal/lcalori0/spack/RCM_spack_deploy/deploy/davide/install/linux-centos7-ppc64le/gcc-4.8.5/font-adobe-75dpi-1.0.3-b6brxnjprny6wofp3eh7qmgrfng5sbkp'

1 error found in build log:
     66    /usr/convex/getsysinfo =
     67    
     68    UNAME_MACHINE = ppc64le
     69    UNAME_RELEASE = 3.10.0-862.3.2.el7.ppc64le
     70    UNAME_SYSTEM  = Linux
     71    UNAME_VERSION = #1 SMP Tue May 22 03:45:03 BST 2018
  >> 72    configure: error: cannot guess build type; you must specify one


```

### Platform and user environment

Please report your OS here:
```commandline
$ uname -a 
Linux davidefe02 3.10.0-862.3.2.el7.ppc64le #1 SMP Tue May 22 03:45:03 BST 2018 ppc64le ppc64le ppc64le GNU/Linux

$ lsb_release -d
Description:	CentOS Linux release 7.5.1804 (AltArch)
``` 






Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/font-adobe-100dpi/package.py b/var/spack/repos/builtin/packages/font-adobe-100dpi/package.py
--- a/var/spack/repos/builtin/packages/font-adobe-100dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-adobe-100dpi/package.py
@@ -6,7 +6,7 @@
 from spack import *
 
 
-class FontAdobe100dpi(Package):
+class FontAdobe100dpi(AutotoolsPackage):
     """X.org adobe-100dpi font."""
 
     homepage = "http://cgit.freedesktop.org/xorg/font/adobe-100dpi"
@@ -23,9 +23,6 @@ class FontAdobe100dpi(Package):
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
-        configure('--prefix={0}'.format(prefix))
-
-        make()
         make('install')
 
         # `make install` copies the files to the font-util installation.
diff --git a/var/spack/repos/builtin/packages/font-adobe-75dpi/package.py b/var/spack/repos/builtin/packages/font-adobe-75dpi/package.py
--- a/var/spack/repos/builtin/packages/font-adobe-75dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-adobe-75dpi/package.py
@@ -6,7 +6,7 @@
 from spack import *
 
 
-class FontAdobe75dpi(Package):
+class FontAdobe75dpi(AutotoolsPackage):
     """X.org adobe-75dpi font."""
 
     homepage = "http://cgit.freedesktop.org/xorg/font/adobe-75dpi"
@@ -23,9 +23,6 @@ class FontAdobe75dpi(Package):
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
-        configure('--prefix={0}'.format(prefix))
-
-        make()
         make('install')
 
         # `make install` copies the files to the font-util installation.


Test patch:
Repository: spack/spack

Issue:
Installation issue: py-numba
v0.35.0 of py-numba (which is the only version listed in package.py) won't build against Python 3.7.x due to apparent API changes in Python.  (This appears to be similar to #9677, although the actual error messages are different.)  There is a newer version of numba available that does build against 3.7.x.

The fix is to add the new numba version and then appropriate `depends_on('python@...)` calls for each version.  Pull request will be coming shortly.


Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/py-llvmlite/package.py b/var/spack/repos/builtin/packages/py-llvmlite/package.py
--- a/var/spack/repos/builtin/packages/py-llvmlite/package.py
+++ b/var/spack/repos/builtin/packages/py-llvmlite/package.py
@@ -12,6 +12,7 @@ class PyLlvmlite(PythonPackage):
     homepage = "http://llvmlite.readthedocs.io/en/latest/index.html"
     url = "https://pypi.io/packages/source/l/llvmlite/llvmlite-0.23.0.tar.gz"
 
+    version('0.25.0', sha256='fd64def9a51dd7dc61913a7a08eeba5b9785522740bec5a7c5995b2a90525025')
     version('0.23.0', '6fc856576a11dbeef71de862f7c419de')
     version('0.20.0', 'f2aa60d0981842b7930ba001b03679ab')
 
diff --git a/var/spack/repos/builtin/packages/py-numba/package.py b/var/spack/repos/builtin/packages/py-numba/package.py
--- a/var/spack/repos/builtin/packages/py-numba/package.py
+++ b/var/spack/repos/builtin/packages/py-numba/package.py
@@ -12,12 +12,22 @@ class PyNumba(PythonPackage):
     homepage = "https://numba.pydata.org/"
     url      = "https://pypi.io/packages/source/n/numba/numba-0.35.0.tar.gz"
 
+    version('0.40.1', sha256='52d046c13bcf0de79dbfb936874b7228f141b9b8e3447cc35855e9ad3e12aa33')
     version('0.35.0', '4f447383406f54aaf18ffaba3a0e79e8')
 
-    depends_on('py-numpy@1.10:',    type=('build', 'run'))
-    depends_on('py-llvmlite@0.20:', type=('build', 'run'))
-    depends_on('py-argparse',       type=('build', 'run'))
-    depends_on('py-funcsigs',       type=('build', 'run'), when='^python@:3.3.99')
+    depends_on('python@3.3:3.7.9999', type=('build', 'run'), when='@0.40.1:')
+    depends_on('python@3.3:3.6.9999', type=('build', 'run'), when='@:0.35.0')
+    depends_on('py-numpy@1.10:1.99', type=('build', 'run'))
+
+    # Note: As of 1 Nov 2018, 0.25 was the latest version of py-llvmlite.
+    # That's why it was chosen as an upper bound in the following depends_on
+    # calls.  If newer versions maintain backwards compatibility, the calls
+    # can be updated accordingly.
+    depends_on('py-llvmlite@0.25', type=('build', 'run'), when='@0.40.1:')
+    depends_on('py-llvmlite@0.20:0.25', type=('build', 'run'), when='@0.35.1')
+
+    depends_on('py-argparse', type=('build', 'run'))
+    depends_on('py-funcsigs', type=('build', 'run'), when='^python@:3.3.99')
     depends_on('py-singledispatch', type=('build', 'run'), when='^python@:3.3.99')
 
     # Version 6.0.0 of llvm had a hidden symbol which breaks numba at runtime.


Test patch:
Repository: spack/spack

Issue:
Installation issue: glib ^python@3:

### Steps to reproduce the issue

```console
$ spack install glib ^python@3: 
```
leads to 

==> Error: ProcessError: Command exited with status 2:
    'make' '-j8' 'install'

6 errors found in build log:
     1590     /usr/bin/install -c -m 644 ./html/right.png
     1591     /usr/bin/install -c -m 644 ./html/style.css
     1592     /usr/bin/install -c -m 644 ./html/tools.html
     1593     /usr/bin/install -c -m 644 ./html/up-insensitive.png
     1594     /usr/bin/install -c -m 644 ./html/up.png
     1595    ImportError: No module named site

which seems to be an error with the python path 

### Platform and user environment

Please report your OS here:
```commandline
$ uname -a 
Darwin orca.llnl.gov 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 21 20:07:39 PDT 2018; root:xnu-3789.73.14~1/RELEASE_X86_64 x86_64
``` 
### Additional information

The same thing happens for 

```console
$ spack install glib ^python@3.6.4 
```
```console
$ spack install glib ^python@3.1.4
```

but not for the python default which is equivalent to 

```console
$ spack install glib ^python@2.7.15
```




Discussion:
FWIW: This seems to be macOS-specific because it works on my Linux machines.
seems to be the same error reported in #8058
same error shows up on linuxmint19 (and possibly on ubuntu 18.04.1)  #9769 

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -72,6 +72,18 @@ def configure_args(self):
                 os.path.basename(self.spec['python'].command.path))
             )
         args.extend(self.enable_or_disable('tracing'))
+        # glib should not use the globally installed gtk-doc. Otherwise,
+        # gtk-doc can fail with Python errors such as "ImportError: No module
+        # named site". This is due to the fact that Spack sets PYTHONHOME,
+        # which can confuse the global Python installation used by gtk-doc.
+        args.append('--disable-gtk-doc-html')
+        # glib uses gtk-doc even though it should be disabled if it can find
+        # its binaries. Override the checks to use the true binary.
+        true = which('true')
+        args.append('GTKDOC_CHECK={0}'.format(true))
+        args.append('GTKDOC_CHECK_PATH={0}'.format(true))
+        args.append('GTKDOC_MKPDF={0}'.format(true))
+        args.append('GTKDOC_REBASE={0}'.format(true))
         return args
 
     @property


Test patch:
Repository: spack/spack

Issue:
gdk-pixbuf build error: "ImportError: No module named site"
### Steps to reproduce the issue

```console
$ spack install gdk-pixbuf
...
5 errors found in build log:
     851     /usr/bin/install -c -m 644 ./html/rn02.html
     852     /usr/bin/install -c -m 644 ./html/style.css
     853     /usr/bin/install -c -m 644 ./html/up-insensitive.png
     854     /usr/bin/install -c -m 644 ./html/up.png
     855    ImportError: No module named site
     856    Makefile:908: recipe for target 'install-data-local' failed
  >> 857    make[4]: *** [install-data-local] Error 1
     858    make[4]: Leaving directory '/tmp/user/spack-stage/spack-stage-zy7tzs/gdk-pixbuf-
            2.31.2/docs/reference/gdk-pixbuf'
...
```

### Platform and user environment

Please report your OS here:
```commandline
$ uname -a
Linux hostx 4.15.0-38-generic #41-Ubuntu SMP Wed Oct 10 10:59:38 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
$ lsb_release -d
Description:    Linux Mint 19 Tara
``` 

### Additional information
Working with the latest pull of the develop branch
[spack-build.out.gdk-pixbuf.txt](https://github.com/spack/spack/files/2596212/spack-build.out.gdk-pixbuf.txt)



Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
--- a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
+++ b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
@@ -32,3 +32,14 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
                                self.prefix.share)
         run_env.prepend_path("XDG_DATA_DIRS",
                              self.prefix.share)
+
+    def configure_args(self):
+        args = []
+        # disable building of gtk-doc files following #9771
+        args.append('--disable-gtk-doc-html')
+        true = which('true')
+        args.append('GTKDOC_CHECK={0}'.format(true))
+        args.append('GTKDOC_CHECK_PATH={0}'.format(true))
+        args.append('GTKDOC_MKPDF={0}'.format(true))
+        args.append('GTKDOC_REBASE={0}'.format(true))
+        return args


Test patch: