![]() ![]() RStudio has a number of added functionalities and a neat GUI, which can make it easier to work with, especially for new users, to familiarise with the scripts, variables, data structure etc. That is completely sufficient for the workshop. If the version you have is command line only (I am not familiar with how it works in linux) and does not permit interactively editing the script on the go and selectively executing parts of the script, then yes, RStudio will make it easier for you.įor Mac and Windows users: the regular R download from CRAN comes equipped with a script editor functionality (File > Open Document to open a previously written script in script editor, or File > New Document to initiate a new one), from which you can easily run code in blocks or in full. The important thing is to have a script editor and to be able to go easily back and forth between the scripts and the console. Any advice on which IDE ? RStudio ? (Nicolas Chiaruttini)Īnswer: Thank you for checking. Question: Do we need to install an IDE for R ? I installed R on linux, but I only have the command line. Apologize for the inconvenience! R RStudio? After that I did not even reinstalled CP 2.2.0 and got it finally running.īeth Cimini's comment: Java 9 is incompatible with CP that's true even for 3.0 (but hopefully not for long). So I set the path for both in the environmental variables manually as JAVA_HOME and JRE_HOME variables. It turned out that Windows lost the environmental variables of the directory for jdk and jre. It seemed that it could not locate the jvm. Startet CP from the command Line and found some errors. Solution: Realized that there were errors written in the command line, but CP closed it so fast, that it was barely visible. Interestingly the ilastik package installed with it seems to work fine, but I try to figure out whats happening. Problem: CellProfiler 2.2.0 seems to have some trouble on my Windows setup and does not start (CellProfiler starts to shut down immediately without error message). Run: sudo pip install -upgrade setuptools Installation and JAVA version In case of error Command "python setup.py egg_info" failed with error code 1 : There are some dependency conflicts I think that often crop up (I'm pretty sure matplotlib is one of them) so I can also send over a list of package versions that I know work nicely on Linux with 2.2 ![]() ![]() Solution: (installation from source did not work, ) So I use a windows VM.īeth Cimini's comments: You have to install from source for that. Problem: There's no easily accessible 2.2.0 version of CellProfiler for Linux. Trouble shooting, Q & A CellProfiler 2.2.0 Installation for Linux machine: ![]()
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