Error in processtrajectories

[MingBit]

Hi,

Thanks for the great cellrouter. :) I'm testing mouse bone marrow sc RNA-seq example code from this https://github.com/edroaldo/cellrouter/blob/master/stemid/StemID_BM_CellRouter.md. Everything works fine on my laptop. There is an error when I put them on the workstation (Linux).

Code:

processtrajectories(cellrouter, genes2use, path.rank=ranks[3], 
                                  num.cells = 3, neighs = 1)

Error:

 Error in igraph::induced.subgraph(graph = g, vids = unlist(igraph::neighborhood(graph = g,  : 
  Not a graph object

I found that the main issues come from 'cellrounter@networks = NULL', meaning no Cells_FlowNetwork_all_paths_subnet.gml files generated from CellRounter.Jar.

I checked the java version from my laptop and computer. laptop: java version "1.8.0_161" Java(TM) SE Runtime Environment (build 1.8.0_161-b12) Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)

computer: openjdk version "1.8.0_131" OpenJDK Runtime Environment (build 1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11) OpenJDK 64-Bit Server VM (build 25.131-b11, mixed mode)

Look forward to your response. Thank you.

[edroaldo]

Hi,

Thank you for your interest in our work! You have to have installed the Oracle Java not the OpenJDK. For some reason, the Java code only works on Oracle JDK. My apologies. This link contains instructions to install the Oracle JDK in ubuntu:

https://www.digitalocean.com/community/tutorials/how-to- install-java-with-apt-get-on-ubuntu-16-04

You can follow instructions in the following link to set which Java your computer is using: https://askubuntu.com/questions/315646/update-java-alternatives-vs-update- alternatives-config-java

Also, you may also need to install the following:

install.packages("Vennerable", repos="http://R-Forge.R-project.org")

Please, let me know if that works!

Thanks!

2018-04-05 5:21 GMT-04:00 MingBit notifications@github.com:

Hi,

Thanks for the great cellrouter. :) I'm testing mouse bone marrow sc RNA-seq example code from this https://github.com/edroaldo/cellrouter/blob/master/stemid/ StemID_BM_CellRouter.md http://url. Everything works fine on my laptop. There is an error when I put them on the workstation (Linux).

Code:

processtrajectories(cellrouter, genes2use, path.rank=ranks[3], num.cells = 3, neighs = 1)

Error:

Error in igraph::induced.subgraph(graph = g, vids = unlist(igraph::neighborhood(graph = g, : Not a graph object

I found that the main issues come from 'cellrounter@networks = NULL', meaning no Cells_FlowNetwork_all_paths_subnet.gml files generated from CellRounter.Jar.

I checked the java version from my laptop and computer. laptop: java version "1.8.0_161" Java(TM) SE Runtime Environment (build 1.8.0_161-b12) Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)

computer: openjdk version "1.8.0_131" OpenJDK Runtime Environment (build 1.8.0_131-8u131-b11-2ubuntu1. 16.04.3-b11) OpenJDK 64-Bit Server VM (build 25.131-b11, mixed mode)

Look forward to your response. Thank you.

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-- Edroaldo

[MingBit]

Hi,

Thanks for your fast response. :) I just installed Oracle JDK (Vennerable already installed before) and tested it again. Unfortunately same error occurred.

Here are the generated files from CellRouter.jar

-rwxrwxrwx 1 root root  464 Apr  5 16:42 CellRouter.sh
-rw-r--r-- 1 root root 1,1K Apr  5 16:42 Cells_FlowNetwork_all_paths_subnet_exportGML.R
-rw-r--r-- 1 root root  15K Apr  5 16:42 Cells_FlowNetwork_all_paths_subnet.txt
-rw-r--r-- 1 root root 5,5K Apr  5 16:42 Cells_FlowNetwork_all_paths_totalFlow.txt
-rw-r--r-- 1 root root 132K Apr  5 16:42 Cells_FlowNetwork_all_paths.txt
-rw-r--r-- 1 root root 9,8K Apr  5 16:42 Cells_FlowNetwork_scripts.R
-rw-r--r-- 1 root root 1,5K Apr  5 16:42 Cells_FlowNetwork_scripts.Rout
-rw-r--r-- 1 root root   21 Apr  5 16:42 cell_sinks.txt
-rw-r--r-- 1 root root   25 Apr  5 16:42 cell_sources.txt

So they are the same as testing with OpenJDK. Cells_FlowNetwork_all_paths_subnet.gml is missing.

java version "1.8.0_161" Java(TM) SE Runtime Environment (build 1.8.0_161-b12) Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)

[edroaldo]

I apologize for the inconvenient.Could you please send me your fil e Cells_FlowNetwork_scripts.Rout?

Thanks!

2018-04-05 10:51 GMT-04:00 MingBit notifications@github.com:

Hi,

Thanks for your fast response. :) I just installed Oracle JDK (Vennerable already installed before) and tested it again. Unfortunately same error occurred.

Here are the generated files from CellRouter.jar

-rwxrwxrwx 1 root root 464 Apr 5 16:42 CellRouter.sh -rw-r--r-- 1 root root 1,1K Apr 5 16:42 Cells_FlowNetwork_all_paths_subnet_exportGML.R -rw-r--r-- 1 root root 15K Apr 5 16:42 Cells_FlowNetwork_all_paths_subnet.txt -rw-r--r-- 1 root root 5,5K Apr 5 16:42 Cells_FlowNetwork_all_paths_totalFlow.txt -rw-r--r-- 1 root root 132K Apr 5 16:42 Cells_FlowNetwork_all_paths.txt -rw-r--r-- 1 root root 9,8K Apr 5 16:42 Cells_FlowNetwork_scripts.R -rw-r--r-- 1 root root 1,5K Apr 5 16:42 Cells_FlowNetwork_scripts.Rout -rw-r--r-- 1 root root 21 Apr 5 16:42 cell_sinks.txt -rw-r--r-- 1 root root 25 Apr 5 16:42 cell_sources.txt

So they are the same as testing with OpenJDK. Cells_FlowNetwork_all_paths_subnet.gml is missing.

java version "1.8.0_161" Java(TM) SE Runtime Environment (build 1.8.0_161-b12) Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)

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-- Edroaldo

[MingBit]

Well, there was an error: "No Vennerable package". But it works after I re-installed Vennerable package. Nice work! Thanks a lot. :D P.S. As I tested, it was working with OpenJDK as well. :+1:

[edroaldo]

That's great news! =D Thank you so much for trying our algorithm. Please, let me know if you have any suggestions for improvement!

Thanks!

2018-04-05 12:01 GMT-04:00 MingBit notifications@github.com:

Well, there was an error: "No Vennerable package". But it works after I re-installed Vennerable package. Nice work! Thanks a lot. :D P.S. As I tested, it was working with OpenJDK as well. 👍

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-- Edroaldo