VisR R Server in a Bad State

Question

VisR R Server in a Bad State

salasd opened this issue 3 years ago · 0 comments

@hyounesy I have tried the previous fixes by changing the PATH in the bat file. The below is the console output:

C:\WINDOWS\system32>pushd "C:\Users\18438\Desktop\Seq with katelyn\10x align\VisR.0.9.42"

C:\Users\18438\Desktop\Seq with katelyn\10x align\VisR.0.9.42>java -Drpath="C:\Program Files\R\R-4.1.0\bin\R.exe" -jar VisR.jar
Checking for updates
Response Code : 403
ERROR [2021-10-08 10:32:53,792] [UpdateManager.java:155] [main] java.io.IOException: Server returned HTTP response code: 403 for URL: http://visr.000webhostapp.com/update.php
WARN [2021-10-08 10:32:53,792] [UpdateManager.java:160] [main] Unable to connect to the update server. Please check your internet connection or try again in a few seconds.
Fetching user directory... INFO [2021-10-08 10:32:53,974] [DirectoryManager.java:139] [main] Application Directory: C:\Users\18438\VisR
java.awt.Dimension[width=300,height=650]
java.awt.Dimension[width=145,height=40]
java.awt.Dimension[width=350,height=325]
C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\WINDOWS\Sun\Java\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v9.2\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v9.2\libnvvp;C:\Program Files\AdoptOpenJDK\jdk-11.0.10.9-hotspot\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System32\OpenSSH;C:\Program Files\Microsoft SQL Server\120\Tools\Binn;C:\Program Files\WireGuard;C:\Program Files\RedHat\java-1.8.0-openjdk-1.8.0.232-3\bin;C:\Program Files\RedHat\java-1.8.0-openjdk-1.8.0.232-3\jre\bin;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Users\18438\AppData\Local\Programs\Python\Python39\Scripts;C:\Users\18438\AppData\Local\Programs\Python\Python39;C:\Users\18438\AppData\Local\Microsoft\WindowsApps;C:\Program Files\JetBrains\PyCharm 2020.2.2\bin;C:\Users\18438\AppData\Local\GitHubDesktop\bin;C:\Users\18438\AppData\Local\Programs\Microsoft VS Code\bin;.
INFO [2021-10-08 10:32:56,560] [StartRserve.java:335] [main] First connect try failed with: Cannot connect: Connection refused: connect
INFO [2021-10-08 10:32:56,560] [StartRserve.java:116] [main] waiting for Rserve to start ... (java.lang.ProcessImpl@1ba9117e)
INFO [2021-10-08 10:32:56,576] [StartRserve.java:146] [main] let us try to connect ...
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> _
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> platform x86_64-w64-mingw32
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> arch x86_64
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> os mingw32
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> system x86_64, mingw32
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> status
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> major 4
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> minor 1.0
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> year 2021
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> month 05
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> day 18
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> svn rev 80317
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> language R
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> version.string R version 4.1.0 (2021-05-18)
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> nickname Camp Pontanezen
INFO [2021-10-08 10:32:56,729] [StartRserve.java:61] [Thread-4] Rserve> [1] "getwd(): C:/Users/18438/Desktop/Seq with katelyn/10x align/VisR.0.9.42"
INFO [2021-10-08 10:32:56,776] [StartRserve.java:61] [Thread-4] Rserve> [1] ".libPaths(): C:/Users/18438/VisR/RLibs/4.1.0 C:/Users/18438/Documents/R/win-library/4.1 C:/Program Files/R/R-4.1.0/library"
INFO [2021-10-08 10:32:56,792] [StartRserve.java:61] [Thread-4] Rserve> [1] "Loading package: Rserve"
INFO [2021-10-08 10:32:56,792] [StartRserve.java:61] [Thread-4] Rserve> [1] "Installing package Rserve from http://cloud.r-project.org/src/contrib/Rserve_1.7-3.1.tar.gz"
INFO [2021-10-08 10:32:56,792] [StartRserve.java:61] [Thread-3] Rserve> Installing package into 'C:/Users/18438/VisR/RLibs/4.1.0'
INFO [2021-10-08 10:32:56,792] [StartRserve.java:61] [Thread-3] Rserve> (as 'lib' is unspecified)
INFO [2021-10-08 10:32:56,792] [StartRserve.java:61] [Thread-3] Rserve> trying URL 'http://cloud.r-project.org/src/contrib/Rserve_1.7-3.1.tar.gz'
INFO [2021-10-08 10:32:56,870] [StartRserve.java:61] [Thread-3] Rserve> Content type 'application/x-gzip' length 587943 bytes (574 KB)
INFO [2021-10-08 10:32:57,387] [StartRserve.java:61] [Thread-3] Rserve> ==================================================
INFO [2021-10-08 10:32:57,387] [StartRserve.java:61] [Thread-3] Rserve> downloaded 574 KB
INFO [2021-10-08 10:32:57,387] [StartRserve.java:61] [Thread-3] Rserve>
INFO [2021-10-08 10:32:57,916] [StartRserve.java:61] [Thread-3] Rserve> * installing source package 'Rserve' ...
INFO [2021-10-08 10:32:57,947] [StartRserve.java:61] [Thread-3] Rserve> ** package 'Rserve' successfully unpacked and MD5 sums checked
INFO [2021-10-08 10:32:57,947] [StartRserve.java:61] [Thread-3] Rserve> ** using staged installation
INFO [2021-10-08 10:32:57,947] [StartRserve.java:61] [Thread-3] Rserve> Warning in system("sh ./configure.win") : 'sh' not found
INFO [2021-10-08 10:32:57,947] [StartRserve.java:61] [Thread-3] Rserve> ERROR: configuration failed for package 'Rserve'
INFO [2021-10-08 10:32:57,947] [StartRserve.java:61] [Thread-3] Rserve> * removing 'C:/Users/18438/VisR/RLibs/4.1.0/Rserve'
INFO [2021-10-08 10:32:58,605] [StartRserve.java:159] [main] Try failed with: Cannot connect: Connection refused: connect
INFO [2021-10-08 10:32:59,124] [StartRserve.java:61] [Thread-4] Rserve> [1] "error: Unable to load package Rserve"
INFO [2021-10-08 10:32:59,125] [StartRserve.java:61] [Thread-4] Rserve> (s)top / (i)gnore / ignore (a)ll ? (s/i/a)
INFO [2021-10-08 10:32:59,130] [StartRserve.java:61] [Thread-4] Rserve> [1] "Failed loading package: Rserve"
INFO [2021-10-08 10:32:59,124] [StartRserve.java:61] [Thread-3] Rserve> Warning message:
INFO [2021-10-08 10:32:59,132] [StartRserve.java:61] [Thread-3] Rserve> In install.packages(url, repos = NULL, type = "source", dependencies = TRUE) :
INFO [2021-10-08 10:32:59,132] [StartRserve.java:61] [Thread-3] Rserve> installation of package 'C:/Users/18438/AppData/Local/Temp/RtmpmMaUp1/downloaded_packages/Rserve_1.7-3.1.tar.gz' had non-zero exit status
INFO [2021-10-08 10:32:59,133] [StartRserve.java:61] [Thread-3] Rserve> Error in Rserve(FALSE, args = "--no-save --slave") :
INFO [2021-10-08 10:32:59,133] [StartRserve.java:61] [Thread-3] Rserve> could not find function "Rserve"
INFO [2021-10-08 10:32:59,133] [StartRserve.java:61] [Thread-3] Rserve> Execution halted
INFO [2021-10-08 10:33:01,180] [StartRserve.java:159] [main] Try failed with: Cannot connect: Connection refused: connect
INFO [2021-10-08 10:33:03,770] [StartRserve.java:159] [main] Try failed with: Cannot connect: Connection refused: connect
INFO [2021-10-08 10:33:06,308] [StartRserve.java:159] [main] Try failed with: Cannot connect: Connection refused: connect
INFO [2021-10-08 10:33:08,854] [StartRserve.java:159] [main] Try failed with: Cannot connect: Connection refused: connect
INFO [2021-10-08 10:33:09,355] [StartRserve.java:185] [main] Windows: query registry to find where R is installed ...
INFO [2021-10-08 10:33:09,355] [StartRserve.java:189] [main] reg query HKLM\Software\R-core\R
INFO [2021-10-08 10:33:09,370] [StartRserve.java:58] [Thread-5] R InstallPath = C:\Program Files\R\R-4.1.0
INFO [2021-10-08 10:33:09,370] [StartRserve.java:116] [main] waiting for Rserve to start ... (java.lang.ProcessImpl@6631f5ca)
INFO [2021-10-08 10:33:09,370] [StartRserve.java:146] [main] let us try to connect ...
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> _
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> platform x86_64-w64-mingw32
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> arch x86_64
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> os mingw32
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> system x86_64, mingw32
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> status
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> major 4
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> minor 1.0
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> year 2021
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> month 05
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> day 18
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> svn rev 80317
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> language R
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> version.string R version 4.1.0 (2021-05-18)
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> nickname Camp Pontanezen
INFO [2021-10-08 10:33:09,526] [StartRserve.java:61] [Thread-7] Rserve> [1] "getwd(): C:/Users/18438/Desktop/Seq with katelyn/10x align/VisR.0.9.42"
INFO [2021-10-08 10:33:09,573] [StartRserve.java:61] [Thread-7] Rserve> [1] ".libPaths(): C:/Users/18438/VisR/RLibs/4.1.0 C:/Users/18438/Documents/R/win-library/4.1 C:/Program Files/R/R-4.1.0/library"
INFO [2021-10-08 10:33:09,589] [StartRserve.java:61] [Thread-7] Rserve> [1] "Loading package: Rserve"
INFO [2021-10-08 10:33:09,589] [StartRserve.java:61] [Thread-7] Rserve> [1] "Installing package Rserve from http://cloud.r-project.org/src/contrib/Rserve_1.7-3.1.tar.gz"
INFO [2021-10-08 10:33:09,589] [StartRserve.java:61] [Thread-6] Rserve> Installing package into 'C:/Users/18438/VisR/RLibs/4.1.0'
INFO [2021-10-08 10:33:09,589] [StartRserve.java:61] [Thread-6] Rserve> (as 'lib' is unspecified)
INFO [2021-10-08 10:33:09,589] [StartRserve.java:61] [Thread-6] Rserve> trying URL 'http://cloud.r-project.org/src/contrib/Rserve_1.7-3.1.tar.gz'
INFO [2021-10-08 10:33:09,636] [StartRserve.java:61] [Thread-6] Rserve> Content type 'application/x-gzip' length 587943 bytes (574 KB)
INFO [2021-10-08 10:33:10,393] [StartRserve.java:61] [Thread-6] Rserve> ==================================================
INFO [2021-10-08 10:33:10,393] [StartRserve.java:61] [Thread-6] Rserve> downloaded 574 KB
INFO [2021-10-08 10:33:10,393] [StartRserve.java:61] [Thread-6] Rserve>
INFO [2021-10-08 10:33:10,886] [StartRserve.java:61] [Thread-6] Rserve> * installing source package 'Rserve' ...
INFO [2021-10-08 10:33:10,901] [StartRserve.java:61] [Thread-6] Rserve> ** package 'Rserve' successfully unpacked and MD5 sums checked
INFO [2021-10-08 10:33:10,901] [StartRserve.java:61] [Thread-6] Rserve> ** using staged installation
INFO [2021-10-08 10:33:10,901] [StartRserve.java:61] [Thread-6] Rserve> Warning in system("sh ./configure.win") : 'sh' not found
INFO [2021-10-08 10:33:10,917] [StartRserve.java:61] [Thread-6] Rserve> ERROR: configuration failed for package 'Rserve'
INFO [2021-10-08 10:33:10,917] [StartRserve.java:61] [Thread-6] Rserve> * removing 'C:/Users/18438/VisR/RLibs/4.1.0/Rserve'
INFO [2021-10-08 10:33:11,450] [StartRserve.java:159] [main] Try failed with: Cannot connect: Connection refused: connect
INFO [2021-10-08 10:33:12,077] [StartRserve.java:61] [Thread-7] Rserve> [1] "error: Unable to load package Rserve"
INFO [2021-10-08 10:33:12,077] [StartRserve.java:61] [Thread-7] Rserve> (s)top / (i)gnore / ignore (a)ll ? (s/i/a)
INFO [2021-10-08 10:33:12,077] [StartRserve.java:61] [Thread-7] Rserve> [1] "Failed loading package: Rserve"
INFO [2021-10-08 10:33:12,077] [StartRserve.java:61] [Thread-6] Rserve> Warning message:
INFO [2021-10-08 10:33:12,088] [StartRserve.java:61] [Thread-6] Rserve> In install.packages(url, repos = NULL, type = "source", dependencies = TRUE) :
INFO [2021-10-08 10:33:12,088] [StartRserve.java:61] [Thread-6] Rserve> installation of package 'C:/Users/18438/AppData/Local/Temp/RtmpkVpRSr/downloaded_packages/Rserve_1.7-3.1.tar.gz' had non-zero exit status
INFO [2021-10-08 10:33:12,088] [StartRserve.java:61] [Thread-6] Rserve> Error in Rserve(FALSE, args = "--no-save --slave") :
INFO [2021-10-08 10:33:12,088] [StartRserve.java:61] [Thread-6] Rserve> could not find function "Rserve"
INFO [2021-10-08 10:33:12,089] [StartRserve.java:61] [Thread-6] Rserve> Execution halted
INFO [2021-10-08 10:33:13,985] [StartRserve.java:159] [main] Try failed with: Cannot connect: Connection refused: connect
INFO [2021-10-08 10:33:16,510] [StartRserve.java:159] [main] Try failed with: Cannot connect: Connection refused: connect
INFO [2021-10-08 10:33:19,061] [StartRserve.java:159] [main] Try failed with: Cannot connect: Connection refused: connect
INFO [2021-10-08 10:33:21,608] [StartRserve.java:159] [main] Try failed with: Cannot connect: Connection refused: connect
Cannot load R.
INFO [2021-10-08 10:33:22,409] [PreferenceManager.java:336] [main] Loading user defined preferences...
INFO [2021-10-08 10:33:22,409] [PreferenceManager.java:340] [main] Opening File: C:\Users\18438\VisR\userDefinedPreferencesV2.bin
INFO [2021-10-08 10:33:22,409] [PreferenceManager.java:345] [main] Loading in progress...
INFO [2021-10-08 10:33:22,409] [PreferenceManager.java:348] [main] Closing File: C:\Users\18438\VisR\userDefinedPreferencesV2.bin