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Unni Chokkathukalam

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Sep 6, 2012, 6:42:06 AM9/6/12

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Dear Mariona,

You are getting this error because you have not installed the dependencies required for mzMatch.R to work. To do this follow the instructions on this tutorial - http://mzmatch.sourceforge.net/tutorial.mzmatch.r.advanced.php.

Best Regards,

Unni

On 06/09/12 10:39, id...@googlegroups.com wrote:

ï¿½ Today's Topic Summary

Group: http://groups.google.com/group/ideom/topics

Instalation of R packages [1 Update]

ï¿½Instalation of R packages

Mariona Jove <mariona....@gmail.com> Sep 05 01:06AM -0700 ï¿½

Hi
ï¿½
I am trying to install the IDEOM software in my computer but I have
problems with R packages installation. The error message is the following:
ï¿½
ERROR: dependency 'xcms' is not available for package 'mzmatch.R'
ï¿½
* removing 'C:/R/library/mzmatch.R'
ï¿½
Mensajes de aviso perdidos
ï¿½
1: comando ejecutado 'C:/R/bin/x64/R CMD INSTALL -l "C:/R/library" "mzmatch.R.tar.gz"'
tiene estatus 1
ï¿½
2: In install.packages(pkgs = "mzmatch.R.tar.gz", repos = NULL, type =
"source") :
ï¿½
installation of package ï¿½mzmatch.R.tar.gzï¿½ had non-zero exit status
ï¿½
> library (rJava)
ï¿½
Error : .onLoad failed in loadNamespace() for 'rJava', details:
ï¿½
call: fun(libname, pkgname)
ï¿½
error: JAVA_HOME cannot be determined from the Registry
ï¿½
Error: package/namespace load failed for ï¿½rJavaï¿½
ï¿½
> if (.Platform$OS.type == 'windows' & .Platform$r_arch == 'i386')
{print('Loading XP 32bit startup')
ï¿½
+ .jinit ()}
ï¿½
> library (mzmatch.R)
ï¿½
Error en library(mzmatch.R) : there is no package called ï¿½mzmatch.Rï¿½
ï¿½
> mzmatch.init (4000)
ï¿½
Error: no se pudo encontrar la funciï¿½n "mzmatch.init"
ï¿½
ï¿½
Do you how can I solve it?
ï¿½
Thank you very much
ï¿½
ï¿½
Mariona Jovï¿½

ï¿½

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Post-doctoral Research Assistant
Institute of Molecular, Cell and Systems Biology
B309, Joseph Black Building
University of Glasgow, Glasgow G12 8QQ

Mariona Jove

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Sep 7, 2012, 4:03:07 PM9/7/12

to unni.chok...@glasgow.ac.uk, id...@googlegroups.com

Dear Unni and Darren

Thanks a lot for the information. Finally I could install properly the software.

Best regards

Mariona

El 06/09/2012 12:42, "Unni Chokkathukalam" <unni.chokkathuka...@glasgow.ac.uk> escribió:

Dear Mariona,

You are getting this error because you have not installed the dependencies required for mzMatch.R to work. To do this follow the instructions on this tutorial - http://mzmatch.sourceforge.net/tutorial.mzmatch.r.advanced.php.

Best Regards,

Unni

On 06/09/12 10:39, id...@googlegroups.com wrote:

Today's Topic Summary

Group: http://groups.google.com/group/ideom/topics

Instalation of R packages [1 Update]

Instalation of R packages

Mariona Jove <mariona....@gmail.com> Sep 05 01:06AM -0700

Hi

I am trying to install the IDEOM software in my computer but I have
problems with R packages installation. The error message is the following:

ERROR: dependency 'xcms' is not available for package 'mzmatch.R'

* removing 'C:/R/library/mzmatch.R'

Mensajes de aviso perdidos

1: comando ejecutado 'C:/R/bin/x64/R CMD INSTALL -l "C:/R/library" "mzmatch.R.tar.gz"'
tiene estatus 1

2: In install.packages(pkgs = "mzmatch.R.tar.gz", repos = NULL, type =
"source") :

installation of package ‘mzmatch.R.tar.gz’ had non-zero exit status

> library (rJava)

Error : .onLoad failed in loadNamespace() for 'rJava', details:

call: fun(libname, pkgname)

error: JAVA_HOME cannot be determined from the Registry

Error: package/namespace load failed for ‘rJava’

> if (.Platform$OS.type == 'windows' & .Platform$r_arch == 'i386')
{print('Loading XP 32bit startup')

+ .jinit ()}

> library (mzmatch.R)

Error en library(mzmatch.R) : there is no package called ‘mzmatch.R’

> mzmatch.init (4000)

Error: no se pudo encontrar la función "mzmatch.init"

Do you how can I solve it?

Thank you very much

Mariona Jové

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-- 
Unni Chokkathukalam, PhD
Post-doctoral Research Assistant
Institute of Molecular, Cell and Systems Biology
B309, Joseph Black Building
University of Glasgow, Glasgow G12 8QQ

Mariona Jove

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Sep 10, 2012, 1:03:27 PM9/10/12

to id...@googlegroups.com

Hi
While trying to perform first steps (xcms and mzmatch) for our data, the following error appears.

java.io.FileNotFoundException: highintensity_gapfilled.peakml (El sistema no puede encontrar el archivo especificado)
    at java.io.FileInputStream.open(Native Method)
    at java.io.FileInputStream.<init>(Unknown Source)
    at java.io.FileInputStream.<init>(Unknown Source)
    at mzmatch.ipeak.sort.RelatedPeaks.main(RelatedPeaks.java:257)

We set the memory for IDEOM up to 8000 bytes..Any idea?

Thanks in advance

Mariona

The R dialog follows
> setwd("C:/ideom_examples")
>
> library (rJava)

> if (.Platform$OS.type == 'windows' & .Platform$r_arch == 'i386') {print('Loading XP 32bit startup')
+ .jinit ()}
> library (mzmatch.R)

Loading required package: xcms
Loading required package: mzR
Loading required package: Rcpp
Loading required package: XML
Loading required package: snow
Loading required package: caTools
Loading required package: bitops
Loading required package: ptw
> mzmatch.init (8000)
>
>
>
> MainClasses <- dir ()
> dir.create ("combined_RSD_filtered")
> dir.create ("combined_RSD_rejected")
> dir.create ("combined")
> for (i in 1:length(MainClasses)){FILESf <- dir (MainClasses[i],full.names=TRUE,pattern="\\.peakml$",recursive=TRUE)
+ OUTPUTf <- paste ("combined/",MainClasses[i],".peakml",sep="")
+ if(length(FILESf)>0){mzmatch.ipeak.Combine (i=paste(FILESf,collapse=","),v=T,rtwindow=30,o=OUTPUTf,combination="set",ppm=5,label=paste(MainClasses[i],sep=""))
+ RSDf <- paste ("combined_RSD_filtered/",MainClasses[i],".peakml",sep="")
+ REJf <- paste ("combined_RSD_rejected/",MainClasses[i],".peakml",sep="")
+ if(length(FILESf)>1) mzmatch.ipeak.filter.RSDFilter(i=OUTPUTf,o=RSDf,rejected=REJf,rsd=0,5,v=T) else file.copy(OUTPUTf,RSDf)}}
> INPUTDIR <- "combined_RSD_filtered"
> FILESf <- dir (INPUTDIR,full.names=TRUE,pattern="\\.peakml$")
> mzmatch.ipeak.Combine(i=paste(FILESf,collapse=","),v=T,rtwindow=30,o="combined.peakml",combination="set",ppm=5)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| Combine 1.0.0
|
| libraries:
| - jfreechart    1.0.13
| - itext         2.1.7
| - jama          1.0.2
| - lma           1.4.0
| - cmdline       2.0.0
| - domsax        1.1.0
| - peakml        1.0.0
| - mzmatch       1.0.2
------------------------------------------------------
Options {
v:           true
rtwindow:    30.0
ppm:         5.0
labels:      []
combination: set
o:           null
label:       null
h:           false
i:           [-o, combined.peakml]
}
Loading:
- -o
java.io.FileNotFoundException: -o (El sistema no puede encontrar el archivo especificado)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(Unknown Source)
        at java.io.FileInputStream.<init>(Unknown Source)
        at mzmatch.ipeak.Combine.main(Combine.java:338)
> mzmatch.ipeak.filter.NoiseFilter (i="combined.peakml",o="combined_noisef.peakml",v=T,codadw=0,8)
Error occurred during initialization of VM
Too small initial heap for new size specified
Mensajes de aviso perdidos
comando ejecutado 'java -da -dsa -Xmn1g -Xss160k -XX:+UseParallelGC -XX:ParallelGCThreads=10 -Xms8m -Xmx8m -cp C:/R/library/mzmatch.R/java/mzmatch.jar mzmatch.ipeak.filter.NoiseFilter -i combined.peakml -o combined_noisef.peakml -codadw 0 -v' tiene estatus 1
> mzmatch.ipeak.filter.SimpleFilter(i="combined_noisef.peakml", o="combined_sfdet.peakml", mindetections=3, v=T)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| SimpleFilter 1.0.0
|
| libraries:
| - jfreechart    1.0.13
| - itext         2.1.7
| - jama          1.0.2
| - lma           1.4.0
| - cmdline       2.0.0
| - domsax        1.1.0
| - peakml        1.0.0
| - mzmatch       1.0.2
------------------------------------------------------
Options {
maxretentiontime: -1.0
n:                -1
o:                combined_sfdet.peakml
minmass:          -1.0
h:                false
i:                [combined_noisef.peakml]
minscanid:        -1.0
v:                true
maxintensity:     -1.0
mindetections:    3
ppm:              0.0
databases:        []
rejected:         null
minretentiontime: -1.0
annotations:      []
maxscanid:        -1.0
offset:           0
maxmass:          -1.0
minintensity:     -1.0
}
[ERROR]: the input-file 'combined_noisef.peakml' does not exist.
> mzmatch.ipeak.filter.SimpleFilter(i="combined_sfdet.peakml", o="combined_highintensity.peakml", minintensity=3000, v=T)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| SimpleFilter 1.0.0
|
| libraries:
| - jfreechart    1.0.13
| - itext         2.1.7
| - jama          1.0.2
| - lma           1.4.0
| - cmdline       2.0.0
| - domsax        1.1.0
| - peakml        1.0.0
| - mzmatch       1.0.2
------------------------------------------------------
Options {
maxretentiontime: -1.0
n:                -1
o:                combined_highintensity.peakml
minmass:          -1.0
h:                false
i:                [combined_sfdet.peakml]
minscanid:        -1.0
v:                true
maxintensity:     -1.0
mindetections:    -1
ppm:              0.0
databases:        []
rejected:         null
minretentiontime: -1.0
annotations:      []
maxscanid:        -1.0
offset:           0
maxmass:          -1.0
minintensity:     3000.0
}
[ERROR]: the input-file 'combined_sfdet.peakml' does not exist.
> PeakML.GapFiller(filename = "combined_highintensity.peakml", ionisation = "positive", Rawpath = NULL, outputfile = "highintensity_gapfilled.peakml", ppm = 0, rtwin = 0)
Error: XML content does not seem to be XML, nor to identify a file name 'combined_highintensity.peakml'
Timing stopped at: 0 0 0
Timing stopped at: 0.04 0 0.05
> mzmatch.ipeak.sort.RelatedPeaks (i="highintensity_gapfilled.peakml",v=T,o="mzMatch_output.peakml",basepeaks="mzMatch_basepeaks.peakml",ppm=5,rtwindow=6)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| RelatedPeaks 1.0.0
|
| libraries:
| - jfreechart    1.0.13
| - itext         2.1.7
| - jama          1.0.2
| - lma           1.4.0
| - cmdline       2.0.0
| - domsax        1.1.0
| - peakml        1.0.0
| - mzmatch       1.0.2
------------------------------------------------------
Options {
v:         true
minrt:     -1.0
rtwindow: 6.0
ppm:       5.0
basepeaks: mzMatch_basepeaks.peakml
o:         mzMatch_output.peakml
h:         false
i:         highintensity_gapfilled.peakml
}
loading data
java.io.FileNotFoundException: highintensity_gapfilled.peakml (El sistema no puede encontrar el archivo especificado)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(Unknown Source)
        at java.io.FileInputStream.<init>(Unknown Source)
        at mzmatch.ipeak.sort.RelatedPeaks.main(RelatedPeaks.java:257)
> annot <- paste("relation.id,relation.ship,codadw,charge")
> mzmatch.ipeak.convert.ConvertToText (i="mzMatch_output.peakml",o="mzMATCHoutput.txt",v=T,annotations=annot)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| ConvertToText 1.0.1
|
| libraries:
| - jfreechart    1.0.13
| - itext         2.1.7
| - jama          1.0.2
| - lma           1.4.0
| - cmdline       2.0.0
| - domsax        1.1.0
| - peakml        1.0.0
| - mzmatch       1.0.2
------------------------------------------------------
Options {
v:           true
databases:   []
o:           mzMATCHoutput.txt
annotations: [relation.id, relation.ship, codadw, charge]
h:           false
i:           [mzMatch_output.peakml]
}
[ERROR]: the input-file 'mzMatch_output.peakml' does not exist.
>
>
>

2012/9/7 Mariona Jove <mariona....@gmail.com>

Gavin Blackburn

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Sep 11, 2012, 12:17:10 PM9/11/12

to Mariona Jove, id...@googlegroups.com

Hi Mariona,

Was there an error before that one?

It's saying it can't find the expected file, but I can't tell why from that. Was there was a GCOverhead limit error as well?

Cheers,

Gavin.
________________________________________
From: id...@googlegroups.com [id...@googlegroups.com] On Behalf Of Mariona Jove [mariona....@gmail.com]
Sent: 10 September 2012 18:03
To: id...@googlegroups.com
Subject: Re: [IDEOM forum]: Digest for id...@googlegroups.com - 1 Message in 1 Topic

> annot <- paste("relation.id<http://relation.id>,relation.ship,codadw,charge")

> mzmatch.ipeak.convert.ConvertToText (i="mzMatch_output.peakml",o="mzMATCHoutput.txt",v=T,annotations=annot)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| ConvertToText 1.0.1
|
| libraries:
| - jfreechart 1.0.13
| - itext 2.1.7
| - jama 1.0.2
| - lma 1.4.0
| - cmdline 2.0.0
| - domsax 1.1.0
| - peakml 1.0.0
| - mzmatch 1.0.2
------------------------------------------------------
Options {
v: true
databases: []
o: mzMATCHoutput.txt

annotations: [relation.id<http://relation.id>, relation.ship, codadw, charge]

h: false
i: [mzMatch_output.peakml]
}
[ERROR]: the input-file 'mzMatch_output.peakml' does not exist.
>
>
>

2012/9/7 Mariona Jove <mariona....@gmail.com<mailto:mariona....@gmail.com>>

Dear Unni and Darren

Thanks a lot for the information. Finally I could install properly the software.

Best regards

Mariona

El 06/09/2012 12:42, "Unni Chokkathukalam" <unni.chokkathuka...@glasgow.ac.uk<mailto:unni.chokkathuka...@glasgow.ac.uk>> escribió:

Dear Mariona,

You are getting this error because you have not installed the dependencies required for mzMatch.R to work. To do this follow the instructions on this tutorial - http://mzmatch.sourceforge.net/tutorial.mzmatch.r.advanced.php.

Best Regards,

Unni

On 06/09/12 10:39, id...@googlegroups.com<mailto:id...@googlegroups.com> wrote:
Today's Topic Summary

Group: http://groups.google.com/group/ideom/topics

* Instalation of R packages [1 Update]

Instalation of R packages<http://groups.google.com/group/ideom/t/de00aa15f375d6af>

Mariona Jove <mariona....@gmail.com><mailto:mariona....@gmail.com> Sep 05 01:06AM -0700

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--
Unni Chokkathukalam, PhD
Post-doctoral Research Assistant
Institute of Molecular, Cell and Systems Biology
B309, Joseph Black Building
University of Glasgow, Glasgow G12 8QQ

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