Failing to install starred plugins

[nsrosenqvist]

I'm trying to install starred plugins with apm stars --install on Ubuntu GNOME 14.04 and I get the following error message:

niklas@Wheatley:~$ apm stars --install
Installing atom-color-highlight to /home/niklas/.atom/packages 
gyp info it worked if it ends with ok
gyp info using node-gyp@0.12.2
gyp info using node@0.10.26 | linux | x64
gyp http GET https://gh-contractor-zcbenz.s3.amazonaws.com/atom-shell/dist/v0.11.10/node-v0.11.10.tar.gz
gyp http 200 https://gh-contractor-zcbenz.s3.amazonaws.com/atom-shell/dist/v0.11.10/node-v0.11.10.tar.gz
gyp ERR! UNCAUGHT EXCEPTION 
gyp ERR! stack Error: EPERM, utime '/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10'
gyp ERR! System Linux 3.13.0-32-generic
gyp ERR! command "/opt/atom/resources/app/apm/node_modules/atom-package-manager/bin/node" "/opt/atom/resources/app/apm/node_modules/atom-package-manager/node_modules/node-gyp/bin/node-gyp.js" "install" "--target=0.11.10" "--dist-url=https://gh-contractor-zcbenz.s3.amazonaws.com/atom-shell/dist" "--arch=x64"
gyp ERR! cwd /home/niklas/.atom
gyp ERR! node -v v0.10.26
gyp ERR! node-gyp -v v0.12.2
gyp ERR! This is a bug in `node-gyp`.
gyp ERR! Try to update node-gyp and file an Issue if it does not help:
gyp ERR!     <https://github.com/TooTallNate/node-gyp/issues>

This is my output from apm -v:

apm  0.78.0
npm  1.4.4
node 0.10.26
python 2.7.6
git 1.9.1

[nsrosenqvist]

I found a discussion relating to this on the Atom Discuss forum. I tried the mentioned workaround (delete ~/.atom) and now I get further on with the installation but it still stops. At the end of the error message it says that there is additional information in a debug log but that log doesn't exist:

npm ERR! Additional logging details can be found in:
npm ERR!     /tmp/apm-install-dir-11476-32197-1pjbo1e/npm-debug.log
npm ERR! not ok code 0

niklas@Wheatley:~$ sudo cp /tmp/apm-install-dir-11476-32197-1pjbo1e/npm-debug.log ~/Downloads/npm-debug.log
[sudo] password for niklas: 
cp: cannot stat ‘/tmp/apm-install-dir-11476-32197-1pjbo1e/npm-debug.log’: No such file or directory

This is all the output I can copy from the terminal before the history gets cut off:

/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:52:35: note: v8::Local<v8::Object> node::Buffer::New(const char*, size_t)
 NODE_EXTERN v8::Local<v8::Object> New(const char* data, size_t len);
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:52:35: note:   candidate expects 2 arguments, 5 provided
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:54:35: note: v8::Local<v8::Object> node::Buffer::New(char*, size_t, node::smalloc::FreeCallback, void*)
 NODE_EXTERN v8::Local<v8::Object> New(char* data,
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:54:35: note:   candidate expects 4 arguments, 5 provided
In file included from ../src/main.cc:1:0:
../../nan/nan.h: In function ‘v8::Local<v8::Object> NanNewBufferHandle(const char*, uint32_t)’:
../../nan/nan.h:900:67: error: no matching function for call to ‘New(v8::Isolate*, const char*&, uint32_t&)’
     return node::Buffer::New(v8::Isolate::GetCurrent(), data, size);
                                                                   ^
../../nan/nan.h:900:67: note: candidates are:
In file included from ../../nan/nan.h:179:0,
                 from ../src/main.cc:1:
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:46:35: note: v8::Local<v8::Object> node::Buffer::New(size_t)
 NODE_EXTERN v8::Local<v8::Object> New(size_t length);
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:46:35: note:   candidate expects 1 argument, 3 provided
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:48:35: note: v8::Local<v8::Object> node::Buffer::New(v8::Handle<v8::String>, node::encoding)
 NODE_EXTERN v8::Local<v8::Object> New(v8::Handle<v8::String> string,
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:48:35: note:   candidate expects 2 arguments, 3 provided
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:52:35: note: v8::Local<v8::Object> node::Buffer::New(const char*, size_t)
 NODE_EXTERN v8::Local<v8::Object> New(const char* data, size_t len);
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:52:35: note:   candidate expects 2 arguments, 3 provided
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:54:35: note: v8::Local<v8::Object> node::Buffer::New(char*, size_t, node::smalloc::FreeCallback, void*)
 NODE_EXTERN v8::Local<v8::Object> New(char* data,
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:54:35: note:   candidate expects 4 arguments, 3 provided
In file included from ../src/main.cc:1:0:
../../nan/nan.h: In function ‘v8::Local<v8::Object> NanNewBufferHandle(uint32_t)’:
../../nan/nan.h:904:61: error: no matching function for call to ‘New(v8::Isolate*, uint32_t&)’
     return node::Buffer::New(v8::Isolate::GetCurrent(), size);
                                                             ^
../../nan/nan.h:904:61: note: candidates are:
In file included from ../../nan/nan.h:179:0,
                 from ../src/main.cc:1:
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:46:35: note: v8::Local<v8::Object> node::Buffer::New(size_t)
 NODE_EXTERN v8::Local<v8::Object> New(size_t length);
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:46:35: note:   candidate expects 1 argument, 2 provided
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:48:35: note: v8::Local<v8::Object> node::Buffer::New(v8::Handle<v8::String>, node::encoding)
 NODE_EXTERN v8::Local<v8::Object> New(v8::Handle<v8::String> string,
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:48:35: note:   no known conversion for argument 1 from ‘v8::Isolate*’ to ‘v8::Handle<v8::String>’
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:52:35: note: v8::Local<v8::Object> node::Buffer::New(const char*, size_t)
 NODE_EXTERN v8::Local<v8::Object> New(const char* data, size_t len);
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:52:35: note:   no known conversion for argument 1 from ‘v8::Isolate*’ to ‘const char*’
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:54:35: note: v8::Local<v8::Object> node::Buffer::New(char*, size_t, node::smalloc::FreeCallback, void*)
 NODE_EXTERN v8::Local<v8::Object> New(char* data,
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node_buffer.h:54:35: note:   candidate expects 4 arguments, 2 provided
In file included from ../src/main.cc:1:0:
../../nan/nan.h: In function ‘v8::Local<v8::Object> NanBufferUse(char*, uint32_t)’:
../../nan/nan.h:911:67: error: cannot convert ‘v8::Isolate*’ to ‘char*’ for argument ‘1’ to ‘v8::Local<v8::Object> node::Buffer::Use(char*, uint32_t)’
     return node::Buffer::Use(v8::Isolate::GetCurrent(), data, size);
                                                                   ^
../../nan/nan.h: In function ‘v8::Local<v8::Script> NanCompileScript(v8::Local<v8::String>, const v8::ScriptOrigin&)’:
../../nan/nan.h:937:9: error: ‘v8::ScriptCompiler’ has not been declared
     v8::ScriptCompiler::Source source(s, origin);
         ^
../../nan/nan.h:937:32: error: expected ‘;’ before ‘source’
     v8::ScriptCompiler::Source source(s, origin);
                                ^
../../nan/nan.h:938:16: error: ‘v8::ScriptCompiler’ has not been declared
     return v8::ScriptCompiler::Compile(v8::Isolate::GetCurrent(), &source);
                ^
../../nan/nan.h:938:68: error: ‘source’ was not declared in this scope
     return v8::ScriptCompiler::Compile(v8::Isolate::GetCurrent(), &source);
                                                                    ^
../../nan/nan.h: In function ‘v8::Local<v8::Script> NanCompileScript(v8::Local<v8::String>)’:
../../nan/nan.h:944:9: error: ‘v8::ScriptCompiler’ has not been declared
     v8::ScriptCompiler::Source source(s);
         ^
../../nan/nan.h:944:32: error: expected ‘;’ before ‘source’
     v8::ScriptCompiler::Source source(s);
                                ^
../../nan/nan.h:945:16: error: ‘v8::ScriptCompiler’ has not been declared
     return v8::ScriptCompiler::Compile(v8::Isolate::GetCurrent(), &source);
                ^
../../nan/nan.h:945:68: error: ‘source’ was not declared in this scope
     return v8::ScriptCompiler::Compile(v8::Isolate::GetCurrent(), &source);
                                                                    ^
../../nan/nan.h: At global scope:
../../nan/nan.h:949:18: error: ‘NanUnboundScript’ was not declared in this scope
       v8::Handle<NanUnboundScript> script
                  ^
../../nan/nan.h:949:34: error: template argument 1 is invalid
       v8::Handle<NanUnboundScript> script
                                  ^
../../nan/nan.h: In function ‘v8::Local<v8::Value> NanRunScript(int)’:
../../nan/nan.h:951:18: error: base operand of ‘->’ is not a pointer
     return script->BindToCurrentContext()->Run();
                  ^
../../nan/nan.h: In function ‘v8::Local<v8::Value> NanMakeCallback(v8::Handle<v8::Object>, v8::Handle<v8::Function>, int, v8::Handle<v8::Value>*)’:
../../nan/nan.h:966:60: error: no matching function for call to ‘MakeCallback(v8::Isolate*, v8::Handle<v8::Object>&, v8::Handle<v8::Function>&, int&, v8::Handle<v8::Value>*&)’
         v8::Isolate::GetCurrent(), target, func, argc, argv));
                                                            ^
../../nan/nan.h:966:60: note: candidates are:
In file included from ../../nan/nan.h:178:0,
                 from ../src/main.cc:1:
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:88:35: note: v8::Handle<v8::Value> node::MakeCallback(v8::Handle<v8::Object>, const char*, int, v8::Handle<v8::Value>*)
 NODE_EXTERN v8::Handle<v8::Value> MakeCallback(
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:88:35: note:   candidate expects 4 arguments, 5 provided
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:93:35: note: v8::Handle<v8::Value> node::MakeCallback(v8::Handle<v8::Object>, v8::Handle<v8::String>, int, v8::Handle<v8::Value>*)
 NODE_EXTERN v8::Handle<v8::Value> MakeCallback(
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:93:35: note:   candidate expects 4 arguments, 5 provided
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:98:35: note: v8::Handle<v8::Value> node::MakeCallback(v8::Handle<v8::Object>, v8::Handle<v8::Function>, int, v8::Handle<v8::Value>*)
 NODE_EXTERN v8::Handle<v8::Value> MakeCallback(
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:98:35: note:   candidate expects 4 arguments, 5 provided
In file included from ../src/main.cc:1:0:
../../nan/nan.h: In member function ‘v8::Local<v8::Function> NanCallback::GetFunction() const’:
../../nan/nan.h:629:3: error: ‘EscapableHandleScope’ is not a member of ‘v8’
   v8::EscapableHandleScope scope(v8::Isolate::GetCurrent())
   ^
../../nan/nan.h:1699:5: note: in expansion of macro ‘NanEscapableScope’
     NanEscapableScope();
     ^
../../nan/nan.h:629:28: error: expected ‘;’ before ‘scope’
   v8::EscapableHandleScope scope(v8::Isolate::GetCurrent())
                            ^
../../nan/nan.h:1699:5: note: in expansion of macro ‘NanEscapableScope’
     NanEscapableScope();
     ^
../../nan/nan.h:641:30: error: ‘scope’ was not declared in this scope
 # define NanEscapeScope(val) scope.Escape(_NanEscapeScopeHelper(val))
                              ^
../../nan/nan.h:1700:12: note: in expansion of macro ‘NanEscapeScope’
     return NanEscapeScope(NanNew(handle)->Get(kCallbackIndex)
            ^
../../nan/nan.h: In member function ‘void NanCallback::Call(int, v8::Handle<v8::Value>*) const’:
../../nan/nan.h:1721:5: error: no matching function for call to ‘MakeCallback(v8::Isolate*&, v8::Local<v8::Object>, v8::Local<v8::Function>&, int&, v8::Handle<v8::Value>*&)’
     );
     ^
../../nan/nan.h:1721:5: note: candidates are:
In file included from ../../nan/nan.h:178:0,
                 from ../src/main.cc:1:
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:88:35: note: v8::Handle<v8::Value> node::MakeCallback(v8::Handle<v8::Object>, const char*, int, v8::Handle<v8::Value>*)
 NODE_EXTERN v8::Handle<v8::Value> MakeCallback(
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:88:35: note:   candidate expects 4 arguments, 5 provided
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:93:35: note: v8::Handle<v8::Value> node::MakeCallback(v8::Handle<v8::Object>, v8::Handle<v8::String>, int, v8::Handle<v8::Value>*)
 NODE_EXTERN v8::Handle<v8::Value> MakeCallback(
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:93:35: note:   candidate expects 4 arguments, 5 provided
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:98:35: note: v8::Handle<v8::Value> node::MakeCallback(v8::Handle<v8::Object>, v8::Handle<v8::Function>, int, v8::Handle<v8::Value>*)
 NODE_EXTERN v8::Handle<v8::Value> MakeCallback(
                                   ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:98:35: note:   candidate expects 4 arguments, 5 provided
In file included from ../src/main.cc:1:0:
../../nan/nan.h: In member function ‘v8::Local<v8::Object> NanAsyncWorker::GetFromPersistent(const char*) const’:
../../nan/nan.h:629:3: error: ‘EscapableHandleScope’ is not a member of ‘v8’
   v8::EscapableHandleScope scope(v8::Isolate::GetCurrent())
   ^
../../nan/nan.h:1785:5: note: in expansion of macro ‘NanEscapableScope’
     NanEscapableScope();
     ^
../../nan/nan.h:629:28: error: expected ‘;’ before ‘scope’
   v8::EscapableHandleScope scope(v8::Isolate::GetCurrent())
                            ^
../../nan/nan.h:1785:5: note: in expansion of macro ‘NanEscapableScope’
     NanEscapableScope();
     ^
../../nan/nan.h:641:30: error: ‘scope’ was not declared in this scope
 # define NanEscapeScope(val) scope.Escape(_NanEscapeScopeHelper(val))
                              ^
../../nan/nan.h:1787:12: note: in expansion of macro ‘NanEscapeScope’
     return NanEscapeScope(handle->Get(NanNew(key)).As<v8::Object>());
            ^
../../nan/nan.h: In instantiation of ‘v8::Local<T> NanNew(P) [with T = v8::Integer; P = int]’:
../../nan/nan.h:606:35:   required from here
../../nan/nan.h:334:43: error: invalid conversion from ‘v8::Isolate*’ to ‘int32_t {aka int}’ [-fpermissive]
     return T::New(v8::Isolate::GetCurrent(), arg1);
                                           ^
In file included from /home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:61:0,
                 from ../../nan/nan.h:178,
                 from ../src/main.cc:1:
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/deps/v8/include/v8.h:1936:25: error:   initializing argument 1 of ‘static v8::Local<v8::Integer> v8::Integer::New(int32_t, v8::Isolate*)’ [-fpermissive]
   static Local<Integer> New(int32_t value, Isolate*);
                         ^
In file included from ../src/main.cc:1:0:
../../nan/nan.h:334:50: error: invalid conversion from ‘int’ to ‘v8::Isolate*’ [-fpermissive]
     return T::New(v8::Isolate::GetCurrent(), arg1);
                                                  ^
In file included from /home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:61:0,
                 from ../../nan/nan.h:178,
                 from ../src/main.cc:1:
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/deps/v8/include/v8.h:1936:25: error:   initializing argument 2 of ‘static v8::Local<v8::Integer> v8::Integer::New(int32_t, v8::Isolate*)’ [-fpermissive]
   static Local<Integer> New(int32_t value, Isolate*);
                         ^
In file included from ../src/main.cc:1:0:
../../nan/nan.h: In instantiation of ‘v8::Local<T> NanNew(P) [with T = v8::Boolean; P = bool]’:
../../nan/nan.h:614:35:   required from here
../../nan/nan.h:334:50: error: no matching function for call to ‘v8::Boolean::New(v8::Isolate*, bool&)’
     return T::New(v8::Isolate::GetCurrent(), arg1);
                                                  ^
../../nan/nan.h:334:50: note: candidate is:
In file included from /home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:61:0,
                 from ../../nan/nan.h:178,
                 from ../src/main.cc:1:
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/deps/v8/include/v8.h:5931:17: note: static v8::Handle<v8::Boolean> v8::Boolean::New(bool)
 Handle<Boolean> Boolean::New(bool value) {
                 ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/deps/v8/include/v8.h:5931:17: note:   candidate expects 1 argument, 2 provided
In file included from ../src/main.cc:1:0:
../../nan/nan.h: In instantiation of ‘v8::Local<T> NanNew() [with T = v8::Object]’:
../../nan/nan.h:1677:52:   required from here
../../nan/nan.h:329:44: error: no matching function for call to ‘v8::Object::New(v8::Isolate*)’
     return T::New(v8::Isolate::GetCurrent());
                                            ^
../../nan/nan.h:329:44: note: candidate is:
In file included from /home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/src/node.h:61:0,
                 from ../../nan/nan.h:178,
                 from ../src/main.cc:1:
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/deps/v8/include/v8.h:2279:24: note: static v8::Local<v8::Object> v8::Object::New()
   static Local<Object> New();
                        ^
/home/niklas/.atom/.node-gyp/.node-gyp/0.11.10/deps/v8/include/v8.h:2279:24: note:   candidate expects 0 arguments, 1 provided
make: *** [Release/obj.target/runas/src/main.o] Error 1
gyp ERR! build error 
gyp ERR! stack Error: `make` failed with exit code: 2
gyp ERR! stack     at ChildProcess.onExit (/opt/atom/resources/app/apm/node_modules/atom-package-manager/node_modules/npm/node_modules/node-gyp/lib/build.js:267:23)
gyp ERR! stack     at ChildProcess.EventEmitter.emit (events.js:98:17)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (child_process.js:797:12)
gyp ERR! System Linux 3.13.0-32-generic
gyp ERR! command "node" "/opt/atom/resources/app/apm/node_modules/atom-package-manager/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/pathwatcher/node_modules/runas
gyp ERR! node -v v0.10.26
gyp ERR! node-gyp -v v0.12.2
gyp ERR! not ok 
npm http 304 https://registry.npmjs.org/domelementtype
npm http GET https://registry.npmjs.org/mixto
npm http GET https://registry.npmjs.org/property-accessors
npm http 304 https://registry.npmjs.org/readable-stream
npm http 304 https://registry.npmjs.org/wordwrap
npm http 304 https://registry.npmjs.org/minimist
npm http 304 https://registry.npmjs.org/domhandler
npm http 304 https://registry.npmjs.org/domutils
npm http 304 https://registry.npmjs.org/domutils
npm http 304 https://registry.npmjs.org/argparse
npm http 304 https://registry.npmjs.org/esprima
npm http 304 https://registry.npmjs.org/season
npm http 304 https://registry.npmjs.org/mixto
npm http 304 https://registry.npmjs.org/property-accessors
npm http 304 https://registry.npmjs.org/CSSwhat
npm http 304 https://registry.npmjs.org/oniguruma
npm http GET https://registry.npmjs.org/coffee-script
npm http GET https://registry.npmjs.org/core-util-is
npm http GET https://registry.npmjs.org/isarray/0.0.1
npm http GET https://registry.npmjs.org/string_decoder
npm http GET https://registry.npmjs.org/inherits
npm http GET https://registry.npmjs.org/underscore.string
npm http 304 https://registry.npmjs.org/coffee-script
npm http 304 https://registry.npmjs.org/core-util-is
npm http 304 https://registry.npmjs.org/isarray/0.0.1
npm http 304 https://registry.npmjs.org/string_decoder
npm http 304 https://registry.npmjs.org/inherits
npm http 304 https://registry.npmjs.org/underscore.string
npm ERR! error rolling back Error: ENOTEMPTY, rmdir '/tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/roaster/node_modules/emoji-images/pngs'
npm ERR! error rolling back  markdown-preview@0.96.0 { [Error: ENOTEMPTY, rmdir '/tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/roaster/node_modules/emoji-images/pngs']
npm ERR! error rolling back   errno: 53,
npm ERR! error rolling back   code: 'ENOTEMPTY',
npm ERR! error rolling back   path: '/tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/roaster/node_modules/emoji-images/pngs' }
npm ERR! runas@1.0.1 install: `node-gyp rebuild`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the runas@1.0.1 install script.
npm ERR! This is most likely a problem with the runas package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     node-gyp rebuild
npm ERR! You can get their info via:
npm ERR!     npm owner ls runas
npm ERR! There is likely additional logging output above.

npm ERR! System Linux 3.13.0-32-generic
npm ERR! command "/opt/atom/resources/app/apm/node_modules/atom-package-manager/bin/node" "/opt/atom/resources/app/apm/node_modules/atom-package-manager/node_modules/npm/bin/npm-cli.js" "--globalconfig" "/opt/atom/resources/app/apm/node_modules/atom-package-manager/.apmrc" "--userconfig" "/home/niklas/.atom/.apmrc" "install" "/home/niklas/.atom/.node-gyp/.atom/.apm/markdown-preview/0.96.0/package.tgz" "--target=0.11.10" "--arch=x64"
npm ERR! cwd /tmp/apm-install-dir-11476-32197-1pjbo1e
npm ERR! node -v v0.10.26
npm ERR! npm -v 1.4.4
npm ERR! code ELIFECYCLE
npm ERR! Error: ENOENT, lstat '/tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/roaster/node_modules/js-yaml/node_modules/argparse/node_modules/underscore.string/test/strings.js'
npm ERR! If you need help, you may report this *entire* log,
npm ERR! including the npm and node versions, at:
npm ERR!     <http://github.com/npm/npm/issues>

npm ERR! System Linux 3.13.0-32-generic
npm ERR! command "/opt/atom/resources/app/apm/node_modules/atom-package-manager/bin/node" "/opt/atom/resources/app/apm/node_modules/atom-package-manager/node_modules/npm/bin/npm-cli.js" "--globalconfig" "/opt/atom/resources/app/apm/node_modules/atom-package-manager/.apmrc" "--userconfig" "/home/niklas/.atom/.apmrc" "install" "/home/niklas/.atom/.node-gyp/.atom/.apm/markdown-preview/0.96.0/package.tgz" "--target=0.11.10" "--arch=x64"
npm ERR! cwd /tmp/apm-install-dir-11476-32197-1pjbo1e
npm ERR! node -v v0.10.26
npm ERR! npm -v 1.4.4
npm ERR! path /tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/roaster/node_modules/js-yaml/node_modules/argparse/node_modules/underscore.string/test/strings.js
npm ERR! fstream_path /tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/roaster/node_modules/js-yaml/node_modules/argparse/node_modules/underscore.string/test/strings.js
npm ERR! fstream_type File
npm ERR! fstream_class FileWriter
npm ERR! code ENOENT
npm ERR! errno 34
npm ERR! fstream_stack /opt/atom/resources/app/apm/node_modules/atom-package-manager/node_modules/npm/node_modules/fstream/lib/writer.js:284:26
npm ERR! fstream_stack Object.oncomplete (fs.js:107:15)
npm ERR! Error: ENOENT, lstat '/tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/highlights/node_modules/first-mate/node_modules/season/node_modules/coffee-script/lib/coffee-script/parser.js'
npm ERR! If you need help, you may report this *entire* log,
npm ERR! including the npm and node versions, at:
npm ERR!     <http://github.com/npm/npm/issues>

npm ERR! System Linux 3.13.0-32-generic
npm ERR! command "/opt/atom/resources/app/apm/node_modules/atom-package-manager/bin/node" "/opt/atom/resources/app/apm/node_modules/atom-package-manager/node_modules/npm/bin/npm-cli.js" "--globalconfig" "/opt/atom/resources/app/apm/node_modules/atom-package-manager/.apmrc" "--userconfig" "/home/niklas/.atom/.apmrc" "install" "/home/niklas/.atom/.node-gyp/.atom/.apm/markdown-preview/0.96.0/package.tgz" "--target=0.11.10" "--arch=x64"
npm ERR! cwd /tmp/apm-install-dir-11476-32197-1pjbo1e
npm ERR! node -v v0.10.26
npm ERR! npm -v 1.4.4
npm ERR! path /tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/highlights/node_modules/first-mate/node_modules/season/node_modules/coffee-script/lib/coffee-script/parser.js
npm ERR! fstream_path /tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/highlights/node_modules/first-mate/node_modules/season/node_modules/coffee-script/lib/coffee-script/parser.js
npm ERR! fstream_type File
npm ERR! fstream_class FileWriter
npm ERR! code ENOENT
npm ERR! errno 34
npm ERR! fstream_stack /opt/atom/resources/app/apm/node_modules/atom-package-manager/node_modules/npm/node_modules/fstream/lib/writer.js:284:26
npm ERR! fstream_stack Object.oncomplete (fs.js:107:15)
npm ERR! Error: ENOENT, lstat '/tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/roaster/node_modules/js-yaml/node_modules/argparse/node_modules/underscore/index.html'
npm ERR! If you need help, you may report this *entire* log,
npm ERR! including the npm and node versions, at:
npm ERR!     <http://github.com/npm/npm/issues>

npm ERR! System Linux 3.13.0-32-generic
npm ERR! command "/opt/atom/resources/app/apm/node_modules/atom-package-manager/bin/node" "/opt/atom/resources/app/apm/node_modules/atom-package-manager/node_modules/npm/bin/npm-cli.js" "--globalconfig" "/opt/atom/resources/app/apm/node_modules/atom-package-manager/.apmrc" "--userconfig" "/home/niklas/.atom/.apmrc" "install" "/home/niklas/.atom/.node-gyp/.atom/.apm/markdown-preview/0.96.0/package.tgz" "--target=0.11.10" "--arch=x64"
npm ERR! cwd /tmp/apm-install-dir-11476-32197-1pjbo1e
npm ERR! node -v v0.10.26
npm ERR! npm -v 1.4.4
npm ERR! path /tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/roaster/node_modules/js-yaml/node_modules/argparse/node_modules/underscore/index.html
npm ERR! fstream_path /tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/roaster/node_modules/js-yaml/node_modules/argparse/node_modules/underscore/index.html
npm ERR! fstream_type File
npm ERR! fstream_class FileWriter
npm ERR! code ENOENT
npm ERR! errno 34
npm ERR! fstream_stack /opt/atom/resources/app/apm/node_modules/atom-package-manager/node_modules/npm/node_modules/fstream/lib/writer.js:284:26
npm ERR! fstream_stack Object.oncomplete (fs.js:107:15)
npm ERR! Error: ENOENT, lstat '/tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/highlights/node_modules/first-mate/node_modules/oniguruma/deps/onig/regparse.c'
npm ERR! If you need help, you may report this *entire* log,
npm ERR! including the npm and node versions, at:
npm ERR!     <http://github.com/npm/npm/issues>

npm ERR! System Linux 3.13.0-32-generic
npm ERR! command "/opt/atom/resources/app/apm/node_modules/atom-package-manager/bin/node" "/opt/atom/resources/app/apm/node_modules/atom-package-manager/node_modules/npm/bin/npm-cli.js" "--globalconfig" "/opt/atom/resources/app/apm/node_modules/atom-package-manager/.apmrc" "--userconfig" "/home/niklas/.atom/.apmrc" "install" "/home/niklas/.atom/.node-gyp/.atom/.apm/markdown-preview/0.96.0/package.tgz" "--target=0.11.10" "--arch=x64"
npm ERR! cwd /tmp/apm-install-dir-11476-32197-1pjbo1e
npm ERR! node -v v0.10.26
npm ERR! npm -v 1.4.4
npm ERR! path /tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/highlights/node_modules/first-mate/node_modules/oniguruma/deps/onig/regparse.c
npm ERR! fstream_path /tmp/apm-install-dir-11476-32197-1pjbo1e/node_modules/markdown-preview/node_modules/highlights/node_modules/first-mate/node_modules/oniguruma/deps/onig/regparse.c
npm ERR! fstream_type File
npm ERR! fstream_class FileWriter
npm ERR! code ENOENT
npm ERR! errno 34
npm ERR! fstream_stack /opt/atom/resources/app/apm/node_modules/atom-package-manager/node_modules/npm/node_modules/fstream/lib/writer.js:284:26
npm ERR! fstream_stack Object.oncomplete (fs.js:107:15)
npm ERR! 
npm ERR! Additional logging details can be found in:
npm ERR!     /tmp/apm-install-dir-11476-32197-1pjbo1e/npm-debug.log
npm ERR! not ok code 0

[kevinsawicki]

This looks like an permissions issue thrown by npm. The npm version used by apm has been upgraded several times in the last year so I'm going to close this out optimistically as something fixed by that upgrade.

Please comment if you still see this using Atom 1.0.3+.