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Salvo Comunque's questions

Martin Hope
Salvo Comunque
Asked: 2019-01-09 08:18:03 +0800 CST
  • 1

The issue started after I used my ubuntu hard-drive on other pc, now secondary monitor plugged on VGA stopped to work. I Tried most of the solutions present on Ask Ubuntu, but nothing is fine for my issue.

lshw -c video
*-display                 
   description: VGA compatible controller
   product: GK208B [GeForce GT 710]
   vendor: NVIDIA Corporation
   physical id: 0
   bus info: pci@0000:01:00.0
   version: a1
   width: 64 bits
   clock: 33MHz
   capabilities: pm msi pciexpress vga_controller bus_master cap_list rom
   configuration: driver=nvidia latency=0
   resources: irq:37 memory:de000000-deffffff memory:d0000000-d7ffffff memory:d8000000-d9ffffff ioport:e000(size=128) memory:c0000-dffff

and 

xrandr
Screen 0: minimum 8 x 8, current 1920 x 1080, maximum 16384 x 16384
DVI-D-0 disconnected (normal left inverted right x axis y axis)
HDMI-0 connected primary 1920x1080+0+0 (normal left inverted right x axis y axis) 521mm x 293mm
   1920x1080     60.00*+  59.94  
   1680x1050     59.95  
   1440x900      59.89  
   1280x1024     75.02    60.02  
   1280x960      60.00  
   1280x720      60.00    59.94  
   1152x864      75.00  
   1024x768      75.03    70.07    60.00  
   800x600       75.00    72.19    60.32    56.25  
   640x480       75.00    72.81    59.94    59.93

I think the issue could be in some file settings, indeed while I was try to start ubuntu from bootable USB hard-drive, secondary monitor started to work. How can I to fix it? Thanks in advance.

multiple-monitors nvidia 18.04
Martin Hope
Salvo Comunque
Asked: 2018-08-28 07:52:42 +0800 CST
  • 9

After upgrading from Ubuntu 16 to 18.4, I am not able to install the rJava package in R.

I read other posts like this, but I didn't solve my issue. if I run install.packages("rJava") on R, Results is this:

Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/home/salvatore/R/x86_64-pc-linux-gnu-library/3.5/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/salvatore/R/x86_64-pc-linux-gnu-library/3.5/rJava’

when I run sudo R CMD javareconf:

Java interpreter : /usr/lib/jvm/java-8-oracle/jre/bin/java
Java version     : 1.8.0_181
Java home path   : /usr/lib/jvm/java-8-oracle
Java compiler    : /usr/lib/jvm/java-8-oracle/bin/javac
Java headers gen.: /usr/lib/jvm/java-8-oracle/bin/javah
Java archive tool: /usr/lib/jvm/java-8-oracle/bin/jar

trying to compile and link a JNI program 
detected JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/lib/jvm/java-8-oracle/include -I/usr/lib/jvm/java-8-oracle/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-oNcpyf/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR


JAVA_HOME        : /usr/lib/jvm/java-8-oracle
Java library path: $(JAVA_HOME)/jre/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
Updating Java configuration in /usr/lib/R
Done.

Any help would be welcome.

r java 18.04 rstudio
Martin Hope
Salvo Comunque
Asked: 2018-06-27 15:33:53 +0800 CST
  • 0

I'm learning shell scripting! For the same I've tried downloading the TCGA genome data using curl on ubuntu (Ubuntu 16.04.3 LTS) terminal.

sh. content

#!/bin/sh

echo /0c8a6022-b770-4a83-bac3-b1526a16c89a/;

token=$(<gdc-user-token.2018-06-26T14_36_13.548Z.txt)

export ec=18; while [ $ec -ne 0 ]; do curl -C - -H "X-Auth-Token: $token" 'https://api.gdc.cancer.gov/slicing/view/0c8a6022-b770-4a83-bac3-b1526a16c89a?region=chr9:131270948-131270948' > STAD/chr9:131270948-131270948_C440.TCGA-BR-6453-01A-11D-1800-08.3_gdc_realn.bam; export ec=$?;done

If I run the sh script, downloaded file is empty, without any error message.

But if the run the command directly then it is working fine.

I will appreciate if anyone let me know the mistake I am doing in the script.

scripts command-line sh curl