As the warning message says then the packages you are trying to install are not
available for R v. 2.15.0.
Please update to the latest version of R (v. 3.2.1). This should solve the
issues you have with installing the required packages.
Best,
Thomas
From: Mariana Silva dos Santos [mailto:mariana.silvadossan...@crick.ac.uk]
Sent: 16. juli 2015 12:51
To: TFRD (Thomas Franck Dyrlund)
Subject: Re: MZMine Installation
Dear Thomas,
Thank you for your prompt reply.
I did what you suggested and it worked! Thank you for that!
I have one more question: I installed R 64 bit 2.15.0 and when I try to install
the packages it gives me the following error:
> install.packages(c("rJava", "ptw", "gplots", "baseline", "hyperSpec",
> "ggplot2"))
Installing package(s) into 'C:/Users/msilvad/Documents/R/win-library/2.15'
(as 'lib' is unspecified)
Warning: unable to access index for repository
http://cran.ma.imperial.ac.uk/bin/windows/contrib/2.15
Warning: unable to access index for repository
http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.15
Warning message:
packages 'rJava', 'ptw', 'gplots', 'baseline', 'hyperSpec', 'ggplot2' are not
available (for R version 2.15.0)
Could you please me recommend me a version that will allowed me to install all
the packages for MZmine?
Thank you very much for your attention.
Best,
Mariana
Dr Mariana Santos
Postdoctoral Scientist in Metabolomics
The Francis Crick Institute
Mill Hill Laboratory
The Ridgeway
Mill Hill
London
NW7 1AA
________________________________
From: TFRD (Thomas Franck Dyrlund) <t...@steno.dk<mailto:t...@steno.dk>>
Sent: 16 July 2015 07:22
To: Developer discussion; Mariana Silva dos Santos
Subject: RE: MZMine Installation
Dear Mariana
The error often occurs if you are running 32-bit Java on a 64-bit Windows. I
suggest that you uninstall all Java versions on your computer and then install
the latest 64-bit version from here:
https://www.java.com/en/download/manual.jsp
When you run the "java -version" command it should state 64-bit - otherwise you
are using the 32-bit version.
C:\Users\Administrator>java -version
java version "1.8.0_31"
Java(TM) SE Runtime Environment (build 1.8.0_31-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.31-b07, mixed mode)
Best regards,
Thomas
From: Mariana Silva dos Santos [mailto:mariana.silvadossan...@crick.ac.uk]
Sent: 15. juli 2015 20:58
To:
mzmine-devel@lists.sourceforge.net<mailto:mzmine-devel@lists.sourceforge.net>
Subject: [Mzmine-devel] MZMine Installation
Dear all,
When I tried to stall MZmine, the following error appeared:
Checking physical memory size...
Found 131016 MB memory, 64-bit system
Java heap size set to 65508 MB
Invalid initial heap size: -Xms65508m
The specified size exceeds the maximum representable size.
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Press any key to continue . . .
Here is all the information of the softwares I am using:
1. Your MZmine version.
2. 2.14.2
3. Your OS and its version (32-bit or 64-bit?).
4. 64bit
5. The exact output of the following two commands:
java -version
6. Version 8 uptade 45
R --version
7. 2.15.0 x64
8. Please attach your startMZmine script file, if you changed any settings
in it. If you did not change the settings, let us know that, too.
@echo off
rem This is necessary to access the TOTAL_MEMORY and ADDRESS_WIDTH variables
inside the IF block
setlocal enabledelayedexpansion
rem Obtain the physical memory size and check if we are running on a 32-bit
system.
if exist C:\Windows\System32\wbem\wmic.exe (
echo Checking physical memory size...
rem Get physical memory size from OS
for /f "skip=1" %%p in ('C:\Windows\System32\wbem\wmic.exe os get
totalvisiblememorysize') do if not defined TOTAL_MEMORY set /a TOTAL_MEMORY=%%p
/ 1024
for /f "skip=1" %%x in ('C:\Windows\System32\wbem\wmic.exe cpu get
addresswidth') do if not defined ADDRESS_WIDTH set ADDRESS_WIDTH=%%x
echo Found !TOTAL_MEMORY! MB memory, !ADDRESS_WIDTH!-bit system
) else (
echo Skipping memory size check, because wmic.exe could not be found
set ADDRESS_WIDTH=32
)
rem The HEAP_SIZE variable defines the Java heap size in MB.
rem That is the total amount of memory available to MZmine 2.
rem By default we set this to 1024 MB on 32-bit systems, or
rem half of the physical memory on 64-bit systems.
rem Feel free to adjust the HEAP_SIZE according to your needs.
if %ADDRESS_WIDTH%==32 (
set HEAP_SIZE=1300
) else (
set /a HEAP_SIZE=%TOTAL_MEMORY% / 2
)
echo Java heap size set to %HEAP_SIZE% MB
rem The TMP_FILE_DIRECTORY parameter defines the location where temporary
rem files (parsed raw data) will be placed. Default is %TEMP%, which
rem represents the system temporary directory.
set TMP_FILE_DIRECTORY=%TEMP%
rem Set R environment variables.
set R_HOME=C:\Program Files\R\R-2.15.0
set R_SHARE_DIR=%R_HOME%\share
set R_INCLUDE_DIR=%R_HOME%\include
set R_DOC_DIR=%R_HOME%\doc
set R_LIBS_USER=%USERPROFILE%\Documents\R\win-library\2.15
rem Include R DLLs in PATH.
set PATH=%PATH%;%R_HOME%\bin\x64
rem The directory holding the JRI shared library (libjri.so).
set JRI_LIB_PATH=%R_LIBS_USER%\rJava\jri\i386
rem It is usually not necessary to modify the JAVA_COMMAND parameter, but
rem if you like to run a specific Java Virtual Machine, you may set the
rem path to the java command of that JVM
set JAVA_COMMAND=java
rem It is not necessary to modify the following section
set JAVA_PARAMETERS=-showversion -classpath lib\* -Djava.ext.dirs=
-XX:+UseParallelGC -Djava.io.tmpdir=%TMP_FILE_DIRECTORY% -Xms%HEAP_SIZE%m
-Xmx%HEAP_SIZE%m -Djava.library.path="%JRI_LIB_PATH%"
set MAIN_CLASS=net.sf.mzmine.main.MZmineCore
rem This command starts the Java Virtual Machine
%JAVA_COMMAND% %JAVA_PARAMETERS% %MAIN_CLASS% %*
rem If there was an error, give the user chance to see it
IF ERRORLEVEL 1 pause
1. If your problem is related to R or any of the MZmine modules that use R
(XCMS module, baseline correction etc.), please provide the following
information:
* Are you running the 32-bit or 64-bit version of R?
* Run R from the command-line (this is how MZmine uses R). For 32-bit
Windows, the command will be something like:
* C:\Program Files\R\R-3.1.3\bin\i386\R.exe
or for 64-bit Windows:
C:\Program Files\R\R-3.1.3\bin\x64\R.exe
Then include the output of the following R commands in your report:
.libPaths()
packageDescription("xcms")
packageDescription("ptw")
packageDescription("rJava")
Finally, please let us know the R settings you've configured in your MZmine
startup script for the variables listed above.
Could you please help me with this matter?
All the best,
Mariana
6.
Dr Mariana Santos
Postdoctoral Scientist in Metabolomics
The Francis Crick Institute
Mill Hill Laboratory
The Ridgeway
Mill Hill
London
NW7 1AA
The Francis Crick Institute Limited is a registered charity in England and
Wales no. 1140062 and a company registered in England and Wales no. 06885462,
with its registered office at 215 Euston Road, London NW1 2BE.
The Francis Crick Institute Limited is a registered charity in England and
Wales no. 1140062 and a company registered in England and Wales no. 06885462,
with its registered office at 215 Euston Road, London NW1 2BE.
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