Fwd: [IDEOM forum]: Digest for ideom@googlegroups.com - 1 Message in 1 Topic

25 views

Skip to first unread message

Mariona Jove

unread,

Sep 13, 2012, 10:21:00 AM9/13/12

to id...@googlegroups.com

Hi

Because some problems were detected in initial combined macros, we have run the macros separately. We started with run XCMS and apparently it converted all the mzXML files to peakml files. However, when we tried to run the MZmatch an error appeared. With the first macros there were several warnings (see below).

Any idea?

Thanks

Mariona

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-mingw32/x64 (64-bit)

R es un software libre y viene sin GARANTIA ALGUNA.
Usted puede redistribuirlo bajo ciertas circunstancias.
Escriba 'license()' o 'licence()' para detalles de distribucion.

R es un proyecto colaborativo con muchos contribuyentes.
Escriba 'contributors()' para obtener más información y
'citation()' para saber cómo citar R o paquetes de R en publicaciones.

Escriba 'demo()' para demostraciones, 'help()' para el sistema on-line de ayuda,
o 'help.start()' para abrir el sistema de ayuda HTML con su navegador.
Escriba 'q()' para salir de R.

> 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 (4000)
>
> rawfiles <- dir (full.names=TRUE,pattern="\\.mzXML$",recursive=TRUE)
> outputfiles <- paste(sub(".mzXML$","",rawfiles),".peakml",sep="")
> for (i in 1:length(rawfiles)){xset <- xcmsSet(rawfiles[i], method='centWave', ppm=2, peakwidth=c(5,100), snthresh=3, prefilter=c(3,1000), integrate=1, mzdiff=0,001, verbose.columns=TRUE, fitgauss=FALSE)
+ PeakML.xcms.write.SingleMeasurement (xset=xset,filename=outputfiles[i],ionisation="positive",addscans=2,writeRejected=FALSE,ApodisationFilter=TRUE)}
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
302 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
99 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData15.mzXML
59 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
336 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
102 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData16.mzXML
73 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
300 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
113 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData17.mzXML
85 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
319 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
119 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData18.mzXML
92 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
299 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
111 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData19.mzXML
79 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
285 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
100 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData20.mzXML
71 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
288 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
91 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData21.mzXML
60 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
632 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
252 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData40.mzXML
187 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
637 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
233 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData41.mzXML
178 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
1102 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
358 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData42.mzXML
273 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
954 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
293 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData43.mzXML
221 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
756 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
279 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData44.mzXML
216 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
758 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
312 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData45.mzXML
237 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
722 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
258 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData46.mzXML
194 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
682 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
253 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData47.mzXML
182 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
659 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
235 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData48.mzXML
178 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
440 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
170 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData64.mzXML
119 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
419 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
148 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData66.mzXML
98 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
392 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
138 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData67.mzXML
105 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
336 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
112 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData69.mzXML
87 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
372 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
151 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData70.mzXML
105 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
378 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
145 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR PROFUND_pos/WorklistData71.mzXML
105 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
347 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
113 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData10.mzXML
82 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
337 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
130 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData11.mzXML
94 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
350 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
122 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData12.mzXML
80 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
311 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
109 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData13.mzXML
79 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
328 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
102 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData14.mzXML
71 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
304 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
106 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData31.mzXML
82 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
354 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
127 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData32.mzXML
90 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
299 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
109 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData33.mzXML
88 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
274 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
97 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData34.mzXML
70 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
289 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
105 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData35.mzXML
74 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
319 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
115 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData36.mzXML
84 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
287 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
96 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData37.mzXML
70 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
314 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
110 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData38.mzXML
70 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
295 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
99 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData39.mzXML
76 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
700 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
261 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData49.mzXML
190 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
621 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
241 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData50.mzXML
184 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
627 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
266 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData51.mzXML
197 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
545 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
218 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData52.mzXML
155 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
599 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
202 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData53.mzXML
154 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
537 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
215 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData54.mzXML
157 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
400 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
139 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData8.mzXML
103 peaks exported.
1:
Detecting mass traces at 2 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
423 m/z ROI's.

Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
150 Peaks.
retrieving raw data
- C:/ideom_examples/./TUMOR SUPERFICIAL_pos/WorklistData9.mzXML
103 peaks exported.
Hubo 44 avisos (use warnings() para verlos)
> warnings()
Warning messages:

1: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
2: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
3: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
4: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
5: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
6: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
7: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
8: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
9: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
10: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
11: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
12: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
13: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
14: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
15: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
16: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
17: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
18: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
19: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
20: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
21: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
22: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
23: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
24: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
25: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
26: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
27: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
28: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
29: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
30: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
31: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
32: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
33: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
34: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
35: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
36: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
37: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
38: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
39: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
40: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
41: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
42: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
43: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL
44: In is.na<http://is.na>(x) :
is.na<http://is.na>() aplicado a un objeto que no es (lista o vector) de tipo 'NULL

> 0){mzmatch.ipeak.Combine (i=paste(FILESf,collapse=","),v=T,rtwindow=30,o=OUTPUTf,combination="set",ppm=5,label=paste(MainClasses[i],sep=""))
Error: inesperado ')' en "0)"
> 1) mzmatch.ipeak.filter.RSDFilter(i=OUTPUTf,o=RSDf,rejected=REJf,rsd=0,5,v=T) else file.copy(OUTPUTf,RSDf)}}
Error: inesperado ')' en "1)"
> 0){mzmatch.ipeak.Combine (i=paste(FILESf,collapse=","),v=T,rtwindow=30,o=OUTPUTf,combination="set",ppm=5,label=paste(MainClasses[i],sep=""))
Error: inesperado ')' en "0)"
> 1) mzmatch.ipeak.filter.RSDFilter(i=OUTPUTf,o=RSDf,rejected=REJf,rsd=0,5,v=T) else file.copy(OUTPUTf,RSDf)}}
Error: inesperado ')' en "1)"
> setwd("C:/ideom_examples")
>
> library (rJava)
> if (.Platform$OS.type == 'windows' & .Platform$r_arch == 'i386') {print('Loading XP 32bit startup')
+ .jinit ()}
> library (mzmatch.R)
> mzmatch.init (4000)
>
> MainClasses <- dir ()
> dir.create ("combined_RSD_filtered")
Mensajes de aviso perdidos
In dir.create("combined_RSD_filtered") :
'combined_RSD_filtered' already exists
> dir.create ("combined_RSD_rejected")
Mensajes de aviso perdidos
In dir.create("combined_RSD_rejected") :
'combined_RSD_rejected' already exists
> dir.create ("combined")
Mensajes de aviso perdidos
In dir.create("combined") : 'combined' already exists
> 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)}}
------------------------------------------------------
| 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: PROFUND_pos.peakml
label: PROFUND_pos
h: false
i: [TUMOR, PROFUND_pos/WorklistData15.peakml, TUMOR, PROFUND_pos/WorklistData16.peakml, TUMOR, PROFUND_pos/WorklistData17.peakml, TUMOR, PROFUND_pos/WorklistData18.peakml, TUMOR, PROFUND_pos/WorklistData19.peakml, TUMOR, PROFUND_pos/WorklistData20.peakml, TUMOR, PROFUND_pos/WorklistData21.peakml, TUMOR, PROFUND_pos/WorklistData40.peakml, TUMOR, PROFUND_pos/WorklistData41.peakml, TUMOR, PROFUND_pos/WorklistData42.peakml, TUMOR, PROFUND_pos/WorklistData43.peakml, TUMOR, PROFUND_pos/WorklistData44.peakml, TUMOR, PROFUND_pos/WorklistData45.peakml, TUMOR, PROFUND_pos/WorklistData46.peakml, TUMOR, PROFUND_pos/WorklistData47.peakml, TUMOR, PROFUND_pos/WorklistData48.peakml, TUMOR, PROFUND_pos/WorklistData64.peakml, TUMOR, PROFUND_pos/WorklistData66.peakml, TUMOR, PROFUND_pos/WorklistData67.peakml, TUMOR, PROFUND_pos/WorklistData69.peakml, TUMOR, PROFUND_pos/WorklistData70.peakml, TUMOR, PROFUND_pos/WorklistData71.peakml]
}
Loading:
- TUMOR
java.io.FileNotFoundException: TUMOR (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)
Error occurred during initialization of VM
Too small initial heap for new size specified
------------------------------------------------------
| 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: SUPERFICIAL_pos.peakml
label: SUPERFICIAL_pos
h: false
i: [TUMOR, SUPERFICIAL_pos/WorklistData10.peakml, TUMOR, SUPERFICIAL_pos/WorklistData11.peakml, TUMOR, SUPERFICIAL_pos/WorklistData12.peakml, TUMOR, SUPERFICIAL_pos/WorklistData13.peakml, TUMOR, SUPERFICIAL_pos/WorklistData14.peakml, TUMOR, SUPERFICIAL_pos/WorklistData31.peakml, TUMOR, SUPERFICIAL_pos/WorklistData32.peakml, TUMOR, SUPERFICIAL_pos/WorklistData33.peakml, TUMOR, SUPERFICIAL_pos/WorklistData34.peakml, TUMOR, SUPERFICIAL_pos/WorklistData35.peakml, TUMOR, SUPERFICIAL_pos/WorklistData36.peakml, TUMOR, SUPERFICIAL_pos/WorklistData37.peakml, TUMOR, SUPERFICIAL_pos/WorklistData38.peakml, TUMOR, SUPERFICIAL_pos/WorklistData39.peakml, TUMOR, SUPERFICIAL_pos/WorklistData49.peakml, TUMOR, SUPERFICIAL_pos/WorklistData50.peakml, TUMOR, SUPERFICIAL_pos/WorklistData51.peakml, TUMOR, SUPERFICIAL_pos/WorklistData52.peakml, TUMOR, SUPERFICIAL_pos/WorklistData53.peakml, TUMOR, SUPERFICIAL_pos/WorklistData54.peakml, TUMOR, SUPERFICIAL_pos/WorklistData8.peakml, TUMOR, SUPERFICIAL_pos/WorklistData9.peakml]
}
Loading:
- TUMOR
java.io.FileNotFoundException: TUMOR (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)
Error occurred during initialization of VM
Too small initial heap for new size specified
Mensajes de aviso perdidos
1: comando ejecutado 'java -da -dsa -Xmn1g -Xss160k -XX:+UseParallelGC -XX:ParallelGCThreads=10 -Xms5m -Xmx5m -cp C:/R/library/mzmatch.R/java/mzmatch.jar mzmatch.ipeak.filter.RSDFilter -i combined/TUMOR PROFUND_pos.peakml -o combined_RSD_filtered/TUMOR PROFUND_pos.peakml -rejected combined_RSD_rejected/TUMOR PROFUND_pos.peakml -rsd 0 -v' tiene estatus 1
2: comando ejecutado 'java -da -dsa -Xmn1g -Xss160k -XX:+UseParallelGC -XX:ParallelGCThreads=10 -Xms5m -Xmx5m -cp C:/R/library/mzmatch.R/java/mzmatch.jar mzmatch.ipeak.filter.RSDFilter -i combined/TUMOR SUPERFICIAL_pos.peakml -o combined_RSD_filtered/TUMOR SUPERFICIAL_pos.peakml -rejected combined_RSD_rejected/TUMOR SUPERFICIAL_pos.peakml -rsd 0 -v' tiene estatus 1
> 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 = "detect", 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: 0.06 0 0.06
> 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<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.
>

2012/9/12 Gavin Blackburn <gavin.b...@strath.ac.uk<mailto:gavin.b...@strath.ac.uk>>
Hi Mariona,

I now know exactly what the problem is. There is a bug with the combined buttons in IDEOM. If you run the macros separately it should run fine. The peak extraction will take a couple of hours depending on your computer so remember to allow enough time to start the next part.

Sorry for the late reply, I'm teaching at a workshop all week.

Cheers,

Gavin.

Sent from my HTC

----- Reply message -----

From: "Mariona Jove" <mariona....@gmail.com<mailto:mariona....@gmail.com>>
To: "Gavin Blackburn" <gavin.b...@strath.ac.uk<mailto:gavin.b...@strath.ac.uk>>
Subject: [IDEOM forum]: Digest for id...@googlegroups.com<mailto:id...@googlegroups.com> - 1 Message in 1 Topic
Date: Wed, Sep 12, 2012 10:32

Hi Gavin

No, we had just started all the software in that moment. We have repeated today, and the same error appears. We have also tryied with the IDEOM_demo_mzXMLfiles and the same error happens (see below).
Do you know if it could come from the installation of R packages?

Thanks for your support

Cheers,

Mariona

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-mingw32/x64 (64-bit)

R es un software libre y viene sin GARANTIA ALGUNA.
Usted puede redistribuirlo bajo ciertas circunstancias.
Escriba 'license()' o 'licence()' para detalles de distribucion.

R es un proyecto colaborativo con muchos contribuyentes.
Escriba 'contributors()' para obtener más información y
'citation()' para saber cómo citar R o paquetes de R en publicaciones.

Escriba 'demo()' para demostraciones, 'help()' para el sistema on-line de ayuda,
o 'help.start()' para abrir el sistema de ayuda HTML con su navegador.
Escriba 'q()' para salir de R.

> setwd("C:/POS")
>
> 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 (4000)
>
>
>
> 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: 0.06 0 0.07
> 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<http://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><http://relation.id>, relation.ship, codadw, charge]
h: false
i: [mzMatch_output.peakml]
}
[ERROR]: the input-file 'mzMatch_output.peakml' does not exist.

2012/9/11 Gavin Blackburn <gavin.b...@strath.ac.uk<mailto:gavin.b...@strath.ac.uk><mailto:gavin.b...@strath.ac.uk<mailto:gavin.b...@strath.ac.uk>>>

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<mailto:id...@googlegroups.com><mailto:id...@googlegroups.com<mailto:id...@googlegroups.com>> [id...@googlegroups.com<mailto:id...@googlegroups.com><mailto:id...@googlegroups.com<mailto:id...@googlegroups.com>>] On Behalf Of Mariona Jove [mariona....@gmail.com<mailto:mariona....@gmail.com><mailto:mariona....@gmail.com<mailto:mariona....@gmail.com>>]

Sent: 10 September 2012 18:03

To: id...@googlegroups.com<mailto:id...@googlegroups.com><mailto:id...@googlegroups.com<mailto:id...@googlegroups.com>>
Subject: Re: [IDEOM forum]: Digest for id...@googlegroups.com<mailto:id...@googlegroups.com><mailto:id...@googlegroups.com<mailto:id...@googlegroups.com>> - 1 Message in 1 Topic

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<http://relation.id><http://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><http://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><mailto:mariona....@gmail.com<mailto:mariona....@gmail.com>><mailto:mariona....@gmail.com<mailto:mariona....@gmail.com><mailto: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><mailto:unni.chokkathuka...@glasgow.ac.uk<mailto:unni.chokkathuka...@glasgow.ac.uk>><mailto:unni.chokkathuka...@glasgow.ac.uk<mailto:unni.chokkathuka...@glasgow.ac.uk><mailto: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><mailto:id...@googlegroups.com<mailto:id...@googlegroups.com>><mailto:id...@googlegroups.com<mailto:id...@googlegroups.com><mailto: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><mailto:mariona....@gmail.com<mailto:mariona....@gmail.com>>><mailto:mariona....@gmail.com<mailto:mariona....@gmail.com><mailto:mariona....@gmail.com<mailto: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

You received this message because you are subscribed to the Google Group ideom.

You can post via email<mailto:id...@googlegroups.com<mailto:id...@googlegroups.com><mailto:id...@googlegroups.com<mailto:id...@googlegroups.com>>>.
To unsubscribe from this group, send<mailto:ideom+un...@googlegroups.com<mailto:ideom%2Bunsu...@googlegroups.com><mailto:ideom%2Bunsu...@googlegroups.com<mailto:ideom%252Buns...@googlegroups.com>>> an empty message.

For more options, visit<http://groups.google.com/group/ideom/topics> this group.

--
You received this message because you are subscribed to the Google Groups "Ideom" group.

For more options, visit this group at http://groups.google.com/group/ideom?hl=en.

--

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

--
You received this message because you are subscribed to the Google Groups "Ideom" group.

To post to this group, send email to id...@googlegroups.com<mailto:id...@googlegroups.com><mailto:id...@googlegroups.com<mailto:id...@googlegroups.com>><mailto:id...@googlegroups.com<mailto:id...@googlegroups.com><mailto:id...@googlegroups.com<mailto:id...@googlegroups.com>>>.
To unsubscribe from this group, send email to ideom+un...@googlegroups.com<mailto:ideom%2Bunsu...@googlegroups.com><mailto:ideom%2Bunsu...@googlegroups.com<mailto:ideom%252Buns...@googlegroups.com>><mailto:ideom%2Bunsu...@googlegroups.com<mailto:ideom%252Buns...@googlegroups.com><mailto:ideom%252Buns...@googlegroups.com<mailto:ideom%25252Bun...@googlegroups.com>>>.

For more options, visit this group at http://groups.google.com/group/ideom?hl=en.

--
You received this message because you are subscribed to the Google Groups "Ideom" group.
To post to this group, send email to id...@googlegroups.com<mailto:id...@googlegroups.com><mailto:id...@googlegroups.com<mailto:id...@googlegroups.com>>.
To unsubscribe from this group, send email to ideom+un...@googlegroups.com<mailto:ideom%2Bunsu...@googlegroups.com><mailto:ideom%2Bunsu...@googlegroups.com<mailto:ideom%252Buns...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/ideom?hl=en.

--
You received this message because you are subscribed to the Google Groups "Ideom" group.
To post to this group, send email to id...@googlegroups.com<mailto:id...@googlegroups.com><mailto:id...@googlegroups.com<mailto:id...@googlegroups.com>>.
To unsubscribe from this group, send email to ideom+un...@googlegroups.com<mailto:ideom%2Bunsu...@googlegroups.com><mailto:ideom%2Bunsu...@googlegroups.com<mailto:ideom%252Buns...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/ideom?hl=en.

Reply all

Reply to author

Forward

0 new messages