Open sanjeevRJMU1 opened 6 years ago
Hi Sanjeev,
I had the exact same issue as you through monocle. This installation issue is likely with gfortran 6.3.0 installed on your mac. You need to re-install gfortran 6.1.
First you have to delete all gfortran 6.3 files first so you can install from the disk image (disk image wont work otherwise);
sudo -r /usr/local/gfortran sudo -r /usr/local/bin/gfortran sudo rm /private/var/db/receipts/com.gnu.gfortran.bom sudo rm /private/var/db/receipts/com.gnu.gfortran.plist
Download here and run the disk image for 6.1 https://gcc.gnu.org/wiki/GFortranBinaries#MacOS
Re-run installation;
install_github("bwlewis/irlba”)
Re-start R
library(irlba)
The error from monocle should be resolved
Hope that helps, Sunny
That resolved the error!!!! Thank you SO much for your help! Sanjeev
Thanks so much @sunwu93 for helping out!
Is there a tar or zip file for 2.3.2?
Hello, I recently found that I will need to update to 2.3.2 however when I try to install from github I get an error. install.packages() will install irlba but install_github() is having some trouble, see the following:
any advice in resolution? Thanks in advance,
UPDATE: Seems I have the same gfortran dependency error now, I think with the above I can get it working again.
UPDATE 2: now getting a new error after installing the disk image of 6.1
-Sejiro
Thanks @sejiro for catching this, a bug!. I'm removing that and re-checking the package now. This was important to catch as I'm trying to get 2.3.2 to cran as soon as possible (just fixed a bunch of issues in prcomp_irlba)...
Try it now. Please let me know if you find anything else, I hope to send it off perhaps tomorrow to CRAN. I unfortunately don't have a macintosh to test on. Do you know if there is a way to rig Travis to test on the mac operating system?
Of course, once I get this on CRAN these problems will go away and you can just install it from there...
I'll be trying this as soon as I get out of journal club! Thanks!
-Sejiro
From: B. W. Lewis notifications@github.com Sent: Wednesday, January 10, 2018 8:55:23 PM To: bwlewis/irlba Cc: Sejiro Littleton; Mention Subject: Re: [bwlewis/irlba] problem updating to 2.3.2 (#28)
Try it now. Please let me know if you find anything else, I hope to send it off perhaps tomorrow to CRAN.
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Still getting the following error, should I go back and update to gfortran 6.3?
yes, I think the 6.3 might work now. Again, it's just a guess as I am unfamiliar with Macintosh...
But good news, the updated package went to cran today and a binary version will appear for Macs soon (usually within a day or two).
On Jan 11, 2018 10:48, "sejiro" notifications@github.com wrote:
Still getting the following error, should I go back and update to gfortran 6.3?
[image: screen shot 2018-01-11 at 10 40 18 am] https://user-images.githubusercontent.com/10656316/34833199-da4d3498-f6bc-11e7-86e7-56615d367a7e.png
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Well, I'm still having some issues but I think I should be running 6.1 as I am operating off OS X el capitan ver. 10.11.6. I guess a binary on cran will appear in a couple days and I can circumvent this issue...but if anyone has any good ideas on how to set up my gcc/gfortran compiler so that it is working appropriately I'd be much obliged.
thanks for all the help -Sejiro
With the mac OS X El Capitan binary for 'irlba' going live on CRAN the package once again plays nice with the 'monocle' package I am using.
That said I am still unsure as to the exact nature of the dyld_stub_binding_helper bug that I am getting trying to install straight from github. If anyone knows a little more about gfortran and mac compilers help with this or a better explanation of the issue would be appreciated.
cheers, -Sejiro
Hi,
I've been trying to run Monocle2.0 and got stuck with the BLAS/LAPACK error. This issue can be resolved apparently by updating the irlba package to 2.3.2. Unfortunately, I am unable to update to the latest version (attached screenshot).
Can you help me resolve this error?
Thanks! Sanjeev