... | ... | @@ -4,7 +4,7 @@ This page lists known recurring issues. If you have a problem with the app, chec |
|
|
|
|
|
### **Installation Problems**
|
|
|
|
|
|
**rJava** :
|
|
|
##### **rJava** :
|
|
|
rJava is an R package that allows R to use libraries written in Java. It requires a Java Development Kit (JDK) installed and findable by R. If you experience issues installing rJava, first make sure that Java is installed. Open a terminal and enter:
|
|
|
```
|
|
|
> java -version
|
... | ... | @@ -43,10 +43,10 @@ option(java-parameters= c("-Xmx4g", "-Xss4m" )) |
|
|
```
|
|
|
Replace the value of the -Xmx parameter by the number of GB you want to allocate.
|
|
|
|
|
|
**java.lang.StackOverflowError**:
|
|
|
##### **java.lang.StackOverflowError**:
|
|
|
On some system with Java 11 and higher, the default stack size of the JVM is too small resulting in java.lang.StackOverflowError. If you get this error, you may want to increase the value of the -Xss parameter.
|
|
|
|
|
|
**RBioFormats**:
|
|
|
##### **RBioFormats**:
|
|
|
This package is the R interface to the Bioformats Java library and therefore depends on rJava. However, it also uses other packages such as fftwtools and tiff that depend on system libraries. Inspect any error message for clues as to which library might be missing. For example, if missing, libfftw and libtiff can be installed on Ubuntu-like systems with:
|
|
|
|
|
|
```
|
... | ... | @@ -55,12 +55,12 @@ This package is the R interface to the Bioformats Java library and therefore dep |
|
|
|
|
|
### **High-throughput microscopy**
|
|
|
|
|
|
**Problem with plate viewer/wrong plate format**
|
|
|
##### **Problem with plate viewer/wrong plate format**
|
|
|
This is likely caused by missing wells. The IDE expects all wells of a given plate to be present in the data. This means that there must be one row per well with the corresponding well identifier column not empty.
|
|
|
|
|
|
### **Container**
|
|
|
|
|
|
**Can't connect to S3 bucket**
|
|
|
##### **Can't connect to S3 bucket**
|
|
|
This can be caused by a DNS issue. If this is the case, set DNS servers when starting the container using the --dns flag, e.g. using Cloudflare's public DNS at 1.1.1.1:
|
|
|
```
|
|
|
> sudo docker run --dns 1.1.1.1 --rm -p 5476:5476 -v /user/home/dir:/data image-data-explorer
|
... | ... | |