Can't build progressiveCactus on OSX (10.7.5)

[deannachurch]

Followed all instructions on the github page. Everything worked fine until I got to the 'make' step.

make
cd submodules && make all
include.mk:20: /Volumes/Macintosh: No such file or directory
include.mk:20: HD: No such file or directory
include.mk:20: 2/Deanna/Google: No such file or directory
include.mk:20: Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk: No such file or directory
make[1]: *** No rule to make target `Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk'.  Stop.
make: *** [all] Error 2

I'm trying to build this on a gdrive directory mounted on my ancillary drive no my Mac- which looks like the problem. But, your page said to report build problems so I'm doing so. I wonder if the spaces in the path are causing the problem:

/Volumes/Macintosh HD 2/Deanna/Google Drive/Cactus/progressiveCactus

[benedictpaten]

Hi Deanna,

Joel or Glenn may comment further, but it looks like it's a path problem, related, as you say, to the mount of the extra disk. It won't install anything outside of the progressiveCactus directory, so I'd suggest building from a location on your main drive.

Cheers,

Benedict

On Wed, May 14, 2014 at 7:32 PM, Deanna Church notifications@github.comwrote:

Followed all instructions on the github page. Everything worked fine until I got to the 'make' step.

make cd submodules && make allinclude.mk:20: /Volumes/Macintosh: No such file or directoryinclude.mk:20: HD: No such file or directoryinclude.mk:20: 2/Deanna/Google: No such file or directoryinclude.mk:20: Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk: No such file or directory make[1]: * No rule to make target `Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk'. Stop. make: * [all] Error 2

I'm trying to build this on a gdrive directory mounted on my ancillary drive no my Mac- which looks like the problem. But, your page said to report build problems so I'm doing so. I wonder if the spaces in the path are causing the problem:

/Volumes/Macintosh HD 2/Deanna/Google Drive/Cactus/progressiveCactus

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/19 .

[glennhickey]

Yeah, it's definitely the spaces in the path. Am trying to fix now.

On Thu, May 15, 2014 at 12:37 PM, Benedict Paten notifications@github.comwrote:

Hi Deanna,

Joel or Glenn may comment further, but it looks like it's a path problem, related, as you say, to the mount of the extra disk. It won't install anything outside of the progressiveCactus directory, so I'd suggest building from a location on your main drive.

Cheers,

Benedict

On Wed, May 14, 2014 at 7:32 PM, Deanna Church notifications@github.comwrote:

Followed all instructions on the github page. Everything worked fine until I got to the 'make' step.

make cd submodules && make allinclude.mk:20: /Volumes/Macintosh: No such file or directoryinclude.mk:20: HD: No such file or directoryinclude.mk:20: 2/Deanna/Google: No such file or directoryinclude.mk:20: Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk: No such file or directory make[1]: * No rule to make target `Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk'. Stop. make: * [all] Error 2

I'm trying to build this on a gdrive directory mounted on my ancillary drive no my Mac- which looks like the problem. But, your page said to report build problems so I'm doing so. I wonder if the spaces in the path are causing the problem:

/Volumes/Macintosh HD 2/Deanna/Google Drive/Cactus/progressiveCactus

— Reply to this email directly or view it on GitHub< https://github.com/glennhickey/progressiveCactus/issues/19> .

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/19#issuecomment-43233784 .

[deannachurch]

Thanks for the reply guys. I may not be able to install on the main drive due to size limitations- my set up is a small, SSD main drive for booting then a large secondary drive for everything else. I have a lot of software installed on HD 2 (which is where I'll need to put this if I install it on my iMac).

On Thu, May 15, 2014 at 9:53 AM, Glenn Hickey notifications@github.comwrote:

Yeah, it's definitely the spaces in the path. Am trying to fix now.

On Thu, May 15, 2014 at 12:37 PM, Benedict Paten notifications@github.comwrote:

Hi Deanna,

Joel or Glenn may comment further, but it looks like it's a path problem, related, as you say, to the mount of the extra disk. It won't install anything outside of the progressiveCactus directory, so I'd suggest building from a location on your main drive.

Cheers,

Benedict

On Wed, May 14, 2014 at 7:32 PM, Deanna Church notifications@github.comwrote:

Followed all instructions on the github page. Everything worked fine until I got to the 'make' step.

make cd submodules && make allinclude.mk:20: /Volumes/Macintosh: No such file or directoryinclude.mk:20: HD: No such file or directoryinclude.mk:20: 2/Deanna/Google: No such file or directoryinclude.mk:20: Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk: No such file or directory make[1]: * No rule to make target `Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk'. Stop. make: * [all] Error 2

I'm trying to build this on a gdrive directory mounted on my ancillary drive no my Mac- which looks like the problem. But, your page said to report build problems so I'm doing so. I wonder if the spaces in the path are causing the problem:

/Volumes/Macintosh HD 2/Deanna/Google Drive/Cactus/progressiveCactus

— Reply to this email directly or view it on GitHub< https://github.com/glennhickey/progressiveCactus/issues/19> .

— Reply to this email directly or view it on GitHub< https://github.com/glennhickey/progressiveCactus/issues/19#issuecomment-43233784>

.

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/19#issuecomment-43235838 .

[benedictpaten]

Okay, NP, sounds like Glenn will get it fixed.

On Thu, May 15, 2014 at 10:27 AM, Deanna Church notifications@github.comwrote:

Thanks for the reply guys. I may not be able to install on the main drive due to size limitations- my set up is a small, SSD main drive for booting then a large secondary drive for everything else. I have a lot of software installed on HD 2 (which is where I'll need to put this if I install it on my iMac).

On Thu, May 15, 2014 at 9:53 AM, Glenn Hickey notifications@github.comwrote:

Yeah, it's definitely the spaces in the path. Am trying to fix now.

On Thu, May 15, 2014 at 12:37 PM, Benedict Paten notifications@github.comwrote:

Hi Deanna,

Joel or Glenn may comment further, but it looks like it's a path problem, related, as you say, to the mount of the extra disk. It won't install anything outside of the progressiveCactus directory, so I'd suggest building from a location on your main drive.

Cheers,

Benedict

On Wed, May 14, 2014 at 7:32 PM, Deanna Church < notifications@github.com>wrote:

Followed all instructions on the github page. Everything worked fine until I got to the 'make' step.

make cd submodules && make allinclude.mk:20: /Volumes/Macintosh: No such file or directoryinclude.mk:20: HD: No such file or directoryinclude.mk:20: 2/Deanna/Google: No such file or directoryinclude.mk:20: Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk: No such file or directory make[1]: * No rule to make target `Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk'. Stop. make: * [all] Error 2

I'm trying to build this on a gdrive directory mounted on my ancillary drive no my Mac- which looks like the problem. But, your page said to report build problems so I'm doing so. I wonder if the spaces in the path are causing the problem:

/Volumes/Macintosh HD 2/Deanna/Google Drive/Cactus/progressiveCactus

— Reply to this email directly or view it on GitHub< https://github.com/glennhickey/progressiveCactus/issues/19> .

— Reply to this email directly or view it on GitHub<

https://github.com/glennhickey/progressiveCactus/issues/19#issuecomment-43233784>

.

— Reply to this email directly or view it on GitHub< https://github.com/glennhickey/progressiveCactus/issues/19#issuecomment-43235838>

.

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/19#issuecomment-43239730 .

[glennhickey]

Hi Deanna,

Thanks for bringing this to our attention.

Looking into it a bit more.... fixing the installation to support spaces may take a while as they cause various problems in many third party tools we include, in addition to our stuff.

I patched it to at least support symlinks though. So a quick workaround is just to link your directory to a path with no spaces. Ex:

cd /somewherepacefree mkdir /Cactus ln -s "/Volumes/Macintosh HD 2/Deanna/Google Drive/Cactus/progressiveCactus" /somewherepacefree/Cactus cd /somewherepacefree/Cactus/progressiveCactus git pull git submodule update --init make

Hope this helps (seems to work on my mac) -Glenn

On Thu, May 15, 2014 at 1:27 PM, Deanna Church notifications@github.comwrote:

Thanks for the reply guys. I may not be able to install on the main drive due to size limitations- my set up is a small, SSD main drive for booting then a large secondary drive for everything else. I have a lot of software installed on HD 2 (which is where I'll need to put this if I install it on my iMac).

On Thu, May 15, 2014 at 9:53 AM, Glenn Hickey notifications@github.comwrote:

Yeah, it's definitely the spaces in the path. Am trying to fix now.

On Thu, May 15, 2014 at 12:37 PM, Benedict Paten notifications@github.comwrote:

Hi Deanna,

Joel or Glenn may comment further, but it looks like it's a path problem, related, as you say, to the mount of the extra disk. It won't install anything outside of the progressiveCactus directory, so I'd suggest building from a location on your main drive.

Cheers,

Benedict

On Wed, May 14, 2014 at 7:32 PM, Deanna Church < notifications@github.com>wrote:

Followed all instructions on the github page. Everything worked fine until I got to the 'make' step.

make cd submodules && make allinclude.mk:20: /Volumes/Macintosh: No such file or directoryinclude.mk:20: HD: No such file or directoryinclude.mk:20: 2/Deanna/Google: No such file or directoryinclude.mk:20: Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk: No such file or directory make[1]: * No rule to make target `Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk'. Stop. make: * [all] Error 2

I'm trying to build this on a gdrive directory mounted on my ancillary drive no my Mac- which looks like the problem. But, your page said to report build problems so I'm doing so. I wonder if the spaces in the path are causing the problem:

/Volumes/Macintosh HD 2/Deanna/Google Drive/Cactus/progressiveCactus

— Reply to this email directly or view it on GitHub< https://github.com/glennhickey/progressiveCactus/issues/19> .

— Reply to this email directly or view it on GitHub<

https://github.com/glennhickey/progressiveCactus/issues/19#issuecomment-43233784>

.

— Reply to this email directly or view it on GitHub< https://github.com/glennhickey/progressiveCactus/issues/19#issuecomment-43235838>

.

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/19#issuecomment-43239730 .

[deannachurch]

Thanks for the quick response!

Sent from my iPad

On May 15, 2014, at 11:02 AM, Glenn Hickey notifications@github.com wrote:

Hi Deanna,

Thanks for bringing this to our attention.

Looking into it a bit more.... fixing the installation to support spaces may take a while as they cause various problems in many third party tools we include, in addition to our stuff.

I patched it to at least support symlinks though. So a quick workaround is just to link your directory to a path with no spaces. Ex:

cd /somewherepacefree mkdir /Cactus ln -s "/Volumes/Macintosh HD 2/Deanna/Google Drive/Cactus/progressiveCactus" /somewherepacefree/Cactus cd /somewherepacefree/Cactus/progressiveCactus git pull git submodule update --init make

Hope this helps (seems to work on my mac) -Glenn

On Thu, May 15, 2014 at 1:27 PM, Deanna Church notifications@github.comwrote:

Thanks for the reply guys. I may not be able to install on the main drive due to size limitations- my set up is a small, SSD main drive for booting then a large secondary drive for everything else. I have a lot of software installed on HD 2 (which is where I'll need to put this if I install it on my iMac).

On Thu, May 15, 2014 at 9:53 AM, Glenn Hickey notifications@github.comwrote:

Yeah, it's definitely the spaces in the path. Am trying to fix now.

On Thu, May 15, 2014 at 12:37 PM, Benedict Paten notifications@github.comwrote:

Hi Deanna,

Joel or Glenn may comment further, but it looks like it's a path problem, related, as you say, to the mount of the extra disk. It won't install anything outside of the progressiveCactus directory, so I'd suggest building from a location on your main drive.

Cheers,

Benedict

On Wed, May 14, 2014 at 7:32 PM, Deanna Church < notifications@github.com>wrote:

Followed all instructions on the github page. Everything worked fine until I got to the 'make' step.

make cd submodules && make allinclude.mk:20: /Volumes/Macintosh: No such file or directoryinclude.mk:20: HD: No such file or directoryinclude.mk:20: 2/Deanna/Google: No such file or directoryinclude.mk:20: Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk: No such file or directory make[1]: * No rule to make target `Drive/Cactus/progressiveCactus/submodules/sonLib/include.mk'. Stop. make: * [all] Error 2

I'm trying to build this on a gdrive directory mounted on my ancillary drive no my Mac- which looks like the problem. But, your page said to report build problems so I'm doing so. I wonder if the spaces in the path are causing the problem:

/Volumes/Macintosh HD 2/Deanna/Google Drive/Cactus/progressiveCactus

— Reply to this email directly or view it on GitHub< https://github.com/glennhickey/progressiveCactus/issues/19> .

— Reply to this email directly or view it on GitHub<

https://github.com/glennhickey/progressiveCactus/issues/19#issuecomment-43233784>

.

— Reply to this email directly or view it on GitHub< https://github.com/glennhickey/progressiveCactus/issues/19#issuecomment-43235838>

.

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/19#issuecomment-43239730 .

— Reply to this email directly or view it on GitHub.

[benedictpaten]

Glenn, if you're not going to fix this in the short term, can you update the installation instructions to describe this issue and your workaround? I'm wrangling comments from the bioinformatics submission, and it's important that we address it (and important in general!).

[joelarmstrong]

I think it may be somewhat difficult to fix, since we include external tools in pcactus. Maybe not impossible, but this is a well-known issue with gnu make. There are ways to fix it for the makefiles we have control of (basically adding quotes to everything) but I don't know whether this happens on the tools we don't control.

Stackoverflow, etc.'s solutions are usually "move the directory to a location without spaces", which is sort of unhelpful.

[benedictpaten]

Glenn indicates that the docs now contain instructions on working with spaces in paths by using symlinks. I'm closing this issue for now, as I think it's a reasonable work around.