Build failure in devel: class "workFlow" is not exported by 'namespace:flowCore'

[sneumann]

Hi,
flowUtils fails to build in
http://bioconductor.org/checkResults/devel/bioc-LATEST/flowUtils/malbec1-install.html
due to

Error: class "workFlow" is not exported by 'namespace:flowCore'

btw, a similar issue occurs in
RGLab/CytoML#54

Apparently there was an API change removing workFlow in
RGLab/flowCore@24d8016#diff-7347fe5a0f184f79ef064e92e3beb297L167

Yours,
Steffen

[jacobpwagner]

@sneumann, from my comment on the parallel issue in CytoML: RGLab/CytoML#54

My PR to remove the dependency was merged here weeks ago: e66653c.

However, that commit has to be merged to Bioconductor by @jspidlen. I have notified him of the issue, but until it is fixed through Bioconductor, users can install flowUtils from the GitHub repo, where the dependency is removed.

[jspidlen]

I am aware of this but still don't know how to merge from https://github.com/jspidlen/flowUtils to whatever the BioConductor version is; can someone send me some instructions? And I apologize for my ignorance on this, haven't done anything here in years ... Best, Josef

…

On Mon, May 6, 2019 at 10:42 AM Jake Wagner ***@***.***> wrote: @sneumann <https://github.com/sneumann>, from my comment on the parallel issue in CytoML: RGLab/CytoML#54 <RGLab/CytoML#54> My PR to remove the dependency was merged here weeks ago: e66653c <e66653c>. However, that commit has to be merged to Bioconductor by @jspidlen <https://github.com/jspidlen>. I have notified him of the issue, but until it is fixed through Bioconductor, users can install flowUtils from the GitHub repo, where the dependency is removed. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AADJJWWIQ7CMFTCFKWBD73LPUBUZLANCNFSM4HLA4QDQ> .

[jacobpwagner]

No worries, @jspidlen. I sent instructions to your bd email on Friday I think. Basically you just need to merge the GitHub master branch here to the master branch of git@git.bioconductor.org:packages/flowUtils.git

If you increase the version in the DESCRIPTION file, it should make sure the change gets picked up for upcoming builds.

Alternatively, I can embed the necessary flowUtils code in to CytoML and remove CytoML's dependency on flowUtils, but flowUtils will continue to fail because flowCore::workFlow is removed.

[jspidlen]

Right, now I remember... I tried to do something about it couple weeks ago, ended up not having access to git@git.bioconductor.org:packages/flowUtils.git, so tried to use https://git.bioconductor.org/BiocCredentials/account_activation/ to activate my account, but it told me that my email is not associated with any Bioconductor packages although it should be. So I just gave up. I'll try to see if bioc-devel@r-project.org can help :-(.

…

On Mon, May 6, 2019 at 2:03 PM Jake Wagner ***@***.***> wrote: No worries, @jspidlen <https://github.com/jspidlen>. I sent instructions to your bd email on Friday I think. Basically you just need to merge the GitHub master branch here to the master branch of ***@***.*** :packages/flowUtils.git If you increase the version in the DESCRIPTION file, it should make sure the change gets picked up for upcoming builds. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AADJJWXPBAESRICED7FF5WTPUCMI3ANCNFSM4HLA4QDQ> .