problem updating to 2.3.2

[sanjeevRJMU1]

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

[sunnyzwu]

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

[sanjeevRJMU1]

That resolved the error!!!! Thank you SO much for your help!
Sanjeev

[bwlewis]

Thanks so much @sunwu93 for helping out!

[muktad]

Is there a tar or zip file for 2.3.2?

[sejiro]

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

[bwlewis]

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)...

[bwlewis]

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...

[sejiro]

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. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bwlewis_irlba_issues_28-23issuecomment-2D356799288&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=xS_0zXxZJsFQ7f1lgrTeXmXrT-bn8nm3zMMON847H4I&m=9lRhsKno-J487OZgllceN1laaXIEeQCsWwDdyqMR6c4&s=_YDJitiO_Qj-uVdrZCLaMNd11_tuXYwSfkIzjMJa-MI&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AKKaPCdivApURGhN5wWN6WyxckZ2EhhOks5tJWoLgaJpZM4QfrtT&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=xS_0zXxZJsFQ7f1lgrTeXmXrT-bn8nm3zMMON847H4I&m=9lRhsKno-J487OZgllceN1laaXIEeQCsWwDdyqMR6c4&s=GuHAQA09GLcnqoDE6aRQAKnk0-0F3gUYoRMNp5o0ZBk&e=>.

[sejiro]

Still getting the following error, should I go back and update to gfortran 6.3?

[bwlewis]

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> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#28 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAIsnjQmOlIRto0-II5F-ubNFVXKfzjLks5tJi1TgaJpZM4QfrtT> .

[sejiro]

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

[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