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rietho / IPO

A Tool for automated Optimization of XCMS Parameters
http://bioconductor.org/packages/IPO/
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IPO test fail with R3.2.0 (2015-04-16) #12

Closed tobigithub closed 7 years ago

tobigithub commented 9 years ago

Hi, I try to run the IPO code from folder test:

BiocGenerics:::testPackage("IPO") Error: package ‘BiocGenerics’ was built before R 3.0.0: please re-install it

setRepositories() install.packages("BioGenerics") Warning message: package ‘BioGenerics’ is not available (for R version 3.2.0)

just to let you know. Tobias

glibiseller commented 9 years ago

Hi,

If "BiocGenerics:::testPackage("IPO")" does not work you can find the actual test-script under https://github.com/glibiseller/IPO/tree/master/inst/unitTests.

What does your sessionInfo() return? I get BiocGenerics_0.14.0 within "other attached packages".

best regards, Gunnar

tobigithub commented 9 years ago

Hi, actually until somebody can show that for all R version clean installations work, I suspect IPO will only work with specific R versions. The good thing is IPO runs under WINDOWS XP with R3.03 see: https://github.com/glibiseller/IPO/issues/16

I tried a number of packages starting in R2, R3.0 R3.2 etc under WIN7 and most of them give errors the one way or the other, I am quite sure R experts can solve many of the issues, common R users not that easy.

After removing the complete R-directory and R-library and a complete reinstall with this old R3.2.0 version I got this additional error below. These errors come and go and change from time to time. Its R, basically reminds me of the "DLL hell" from Windows.

I think one would need to built a tree with all R versions and then always test and update that with all current packages. Unit testing and dependency testing is quite common in other "languages", its probably not very common for R where every month or so a new version comes out. Well now its the "R dependency hell". http://blog.revolutionanalytics.com/2014/10/introducing-rrt.html

Cheers Tobias

glibiseller commented 9 years ago

Hi,

thanks Tobias for testing all these different R versions. At the moment I'm only running R 3.2.1 on Win7 and Linux which works fine.

I always wait some time before installing the newest R-version exactly because of these dependencies.

Maybe it would be good to add system-setups that work to the readme-file at https://github.com/glibiseller/IPO.

What do you think? Cheers Gunnar

tobigithub commented 9 years ago

Hi, Its a good idea to keep a log of confirmed versions, I also confirmed WIN7, R3.1.2, IPO works. In principle it could also go into the IPO WIKI https://github.com/glibiseller/IPO/wiki Cheers Tobias

glibiseller commented 9 years ago

Hi,

good idea. I already created a wiki-page regarding system-configurations. https://github.com/glibiseller/IPO/wiki/known-working-system-configurations

Do you have a WIN7 32 or 64 bit installation?

Maybe we could keep this issue open so people can post their working configurations?

Cheers, Gunnar

sneumann commented 8 years ago

The issue during installation with biocLite() seems to be specific to R-3.2.0, as mentioned here https://stackoverflow.com/questions/30955508/r-cannot-load-package-forecast-due-to-namespace-error/30956549#30956549, and with a technical explanation in this comment: http://stackoverflow.com/questions/32912268/error-in-r-data-table-v1-9-6-function-fread/32959306#32959306

Bottomline is that Windows binary ZIP packages built recently on R-3.2.>=1 do not work on R-3.2.0, that explains why your build from source succeeded.