This file is indexed.

/usr/lib/R/site-library/MALDIquant/NEWS is in r-cran-maldiquant 1.9-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
RELEASE HISTORY OF THE "MALDIquant" PACKAGE
===========================================


CHANGES IN MALDIquant VERSION 1.9 [2014-01-14]:
-----------------------------------------------

NEW FEATURES

* Add `alignSpectra`: a wrapper around `detectPeaks`,
  `determineWarpingFunctions` and `warpMassSpectra` to provide an easier
  workflow.

IMPROVEMENTS

* `filterPeaks`: introduce "mergeWhitelists" argument to additionally keep peaks
  that occur at least in one group. The default behaviour does not changed.
  Please see the man page of `filterPeaks` for details.
* `intensityMatrix`: add "spectra" argument to allow interpolation of missing
  peaks if corresponding spectra is given.
* Replace some `lapply` calls by `mapply` to allow different
  "halfWindowSize" arguments etc.;
  affected methods: `smoothIntensity`, `removeBaseline`, `detectPeaks`.

MODIFICATIONS

* `filterPeaks`: "minFrequency" > 1 and "minNumber" > n is not set
  to 1 or n anymore; only a warning about "empty peak whitelists" is given;
  see also issue #26.
* `filterPeaks`: replace warning about too large "minFrequency" or "minNumber"
  by a warning about "empty peak whitelists".
* `intensityMatrix`: rename first argument to "peaks"
* demo/workflow.R: introduce `alignSpectra`.
* demo/warping.R: adapt to current preferred workflow.
* demo/peaks.R: add smoothing and a few new plots.

DEPRECATED ARGUMENTS/FUNCTIONS

- `intensityMatrix` for MassSpectrum objects.

DEFUNCT ARGUMENTS/FUNCTIONS

* `isMassObject`/`isMassObjectList`: use `isMassSpectrum`, `isMassPeaks`,
  `isMassSpectrumList` or `isMassPeaksList` instead.
* `totalIonCurrent,MassPeaks-method`: TIC of peaks is meaningless.
* `totalIonCurrent<-,MassSpectrum-method`:
  use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize
  MassSpectrum objects.
* `standardizeTotalIonCurrent`:
  use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize
  MassSpectrum objects.
* `calibrate`:
  use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize
  MassSpectrum objects.
* `ltrim`/`rtrim`: use `trim(..., range=c(min, max))` instead.
* `determineWarpingFunctions`, argument "warpingFunction": use "method" argument
  instead.
* `mergeMassPeaks`, argument "fun": use "method" argument instead.
* `mergeMassSpectra`: use `averageMassSpectra`.
* `savitzkyGolay`: use `smoothIntensity(..., method="SavitzkyGolay")` instead.
* `movingAverage`: use `smoothIntensity(..., method="MovingAverage")` instead.
* `transformIntensity`, argument "fun": use "method" argument instead.
* `removeBaseline`, argument "fun": use "method" argument instead.
* `detectPeaks`, argument "fun": use "method" argument instead.

BUGFIXES

* `plot`: fix subtitle for averaged spectra.

INTERNAL CHANGES

* Add `.as.matrix.MassObjectList` to avoid internal dependencies on
  `intensityMatrix`;
  affected functions: `filterPeaks`, `referencePeaks`.
* Add `.as.binary.matrix`.
* Remove man/MALDIquant-internal.Rd.
* Argument "representation" of `setClass` is deprecated since R 3.0.0;
  use "slots" instead.
  affected classes: AbstractMassObject, MassPeaks, MassSpectrum.


CHANGES IN MALDIquant VERSION 1.8 [2013-09-08]:
-----------------------------------------------

NEW FEATURES

* Add `smoothIntensity`: to apply smoothing filters. Supports
  "SavitzkyGolay" and "MovingAverage". `savitzkyGolay` and `movingAverage`
  are now marked as deprecated.
* Add `calibrateIntensity`: to calibrate/normalize intensity values.
  Supports "TIC", "median" and "PQN" calibration/normalization.
  It replaces three similar functions with
  different names: `totalIonCurrent<-`, `standardizeTotalIonCurrent`,
  `calibrate` (these three are marked as deprecated and will be removed in
  future releases).
* Add `averageMassSpectra`: supports "mean", "median" and "sum" aggregation of
  spectra. It replaces `mergeMassSpectra`.
* Add C implementation of colMedians for faster averaging/merging of
  MassSpectrum/MassPeaks objects.
* Add LongVector support; now MALDIquant depends on R >= 3.0.0.

MODIFICATIONS

* MassSpectrum/MassPeaks class: change representation of slots mass, intensity,
  snr to "numeric" (was "vector" before). Should not affect anything. Maybe you
  have to reimport raw data and resave RData files.
* `trim`: replace "minMass" and "maxMass" arguments by new "range" argument.
* `transformIntensity`: add "method" argument (supports "sqrt", "log", "log2",
  "log10"). "fun" argument is deprecated.
* `estimateBaseline`/`removeBaseline`: rename argument method="Median" to
  method="median".
* `determineWarpingFunctions`: add "method" argument (supports "lowess",
  "linear", "quadratic", "cubic"); "warpingFunctions" argument is deprecated.
* `mergeMassPeaks`: add "method" (supports "mean", "median", "sum") argument;
  "fun" argument is deprecated.

DEPRECATED ARGUMENTS/FUNCTIONS

* `isMassObject`/`isMassObjectList`: use `isMassSpectrum`, `isMassPeaks`,
  `isMassSpectrumList` or `isMassPeaksList` instead.
* `totalIonCurrent,MassPeaks-method`: TIC of peaks is meaningless.
* `totalIonCurrent<-,MassSpectrum-method`:
  use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize
  MassSpectrum objects.
* `standardizeTotalIonCurrent`:
  use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize
  MassSpectrum objects.
* `calibrate`:
  use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize
  MassSpectrum objects.
* `ltrim`/`rtrim`: use `trim(..., range=c(min, max))` instead.
* `determineWarpingFunctions`, argument "warpingFunction": use "method" argument
  instead.
* `mergeMassPeaks`, argument "fun": use "method" argument instead.
* `mergeMassSpectra`: use `averageMassSpectra`.
* `savitzkyGolay`: use `smoothIntensity(..., method="SavitzkyGolay")` instead.
* `movingAverage`: use `smoothIntensity(..., method="MovingAverage")` instead.
* `transformIntensity`, argument "fun": use "method" argument instead.
* `removeBaseline`, argument "fun": use "method" argument instead.
* `detectPeaks`, argument "fun": use "method" argument instead.

REMOVED FUNCTIONS

* `iplot`: because it throws NOTEs on CRAN's R CMD check and the most
  important function `grDevices::getGraphicEvents` behaves
  different on Unix/Windows platform (some keys don't working) and contains some
  nasty bugs, e.g.: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15208
  Also the "zoom" R package provides similar functionality.

BUG FIXES

* `totalIonCurrent`: fix calculation by estimating the integral; fixes #29.
  affected functions: `totalIonCurrent`,
    `calibrateIntensity(..., method="TIC")`.
* `filterPeaks`: reduce minNumber to length(l) to avoid complete removal
  of peaks; fixes #26.
* src/snip.c: fix some segmention faults because of a missing
  PROTECT for "duplicate" call.
  affected functions: `estimateBasline/removeBaseline(..., method="SNIP")`
- Add `import("methods")` to NAMESPACE (fixes #36).

INTERNAL CHANGES

* Remove internal `imputeMass`.
* Remove internal `.replaceNonEmptyMassObjects`.
* `approxfun`: returns NA for empty MassSpectrum objects.
* `[` (subset method): little speed up by calling `which` to evaluate logical
  expressions only once.
* Use integer values where possible.
* Modify C written functions to support LongVectors; closes #13;
  now MALDIquant depends on R >= 3.0.0.


CHANGES IN MALDIquant VERSION 1.7 [2013-05-23]:
-----------------------------------------------

NEW FEATURES

* Add `isRegular` method to test MassSpectrum objects for regular increasing
  mass values/intervals; closes #23.
* Add `savitzkyGolay`, Savitzky-Golay Smoothing Filter.
* Add memory usage to `show` output.
* `iplot`: add horizontal distance measurement (using left mouse clicks).
* `filterPeaks`: add "minNumber" argument to allow an absolute threshold for
  filtering; closes #21.
* demo/workflow.R: add raw data check.

IMPROVEMENTS

* demo/workflow.R: replace moving average smoother by Savitzky-Golay-Filter.
* `.estimateBaselineSnip`: support decreasing/increasing clipping window;
  controlled by new argument "decreasing"; use a decreasing window per default
  to get a smoother baseline; (use decreasing=FALSE to get the old behaviour).
* `isEmpty`: treat spectra with only zeros as intensity values as empty ones.
* `movingAverage`: left/right extrema now calculated for 0:windowSize and
  (n-windowSize+1):n (before they were set to NA).

BUG FIXES

* `filterPeaks`: doesn't round (floor) minFrequency argument anymore; led to
  unexpected results; fixes #22.
* `mergeMassSpectra`: empty MassSpectrum objects are ignored now
  (but if all objects are empty `mergeMassSpectra` will return an empty
  MassSpectrum object, too); fixes #20.
* `.mergeMetaData`: fix merging of lists with different lengths; fixes #17.
  affected functions: `mergeMassPeaks`, `mergeMassSpectra`.
* `.doByLabels: preserve order of non-factor labels; fixes #19;
  affected functions: `filterPeaks`, `mergeMassPeaks`, `mergeMassSpectra`.
* `totalIonCurrent`/`isEmpty`: fix integer overflow; fixes #25.
* `totalIonCurrent<-`: fix handling of empty spectra; fixes #15.
* Remove LICENSE file.

INTERNAL CHANGES

* Replace all `paste(..., sep="")` calls by `paste0`;
  now MALDIquant depends on R >= 2.15.
* Replace all `.C` interfaces by `.Call`.


CHANGES IN MALDIquant VERSION 1.6 [2013-03-01]:
-----------------------------------------------

NEW FEATURES

* Add interactive plot method: `iplot`.
* Add TopHat baseline estimation: `estimateBaseline(..., method="TopHat")`/
  `removeBaseline(..., method="TopHat")`.

IMPROVEMENTS

* Include tests in inst/tests.

BUG FIXES

* `.which.closest`: rounding .5 to the next highest integer (before: to the next
  lowest one); affected functions: `labelPeaks`.
* `.doByLabels`: fix an error that occurred if all labels were unique
  (fixes #1); affected functions: `filterPeaks`, `mergeMassPeaks`,
  `mergeMassSpectra`.
* `estimateBaseline(..., method="Median")`: do not allow a window size > n
  (fixes #4).


CHANGES IN MALDIquant VERSION 1.5 [2012-12-06]:
-----------------------------------------------

NEW FEATURES

* Add `movingAverage`.
* `labelPeaks`: add labels argument.

IMPROVEMENTS

* `detectPeaks`: only throw an error if windowSize > length
  (windowSize == length is no error anymore).
* `.doByLabels`: drop unused levels of argument "labels";
  affected functions: `filterPeaks`, `mergeMassPeaks`, `mergeMassSpectra`.
* Rewrite `localMaxima` in C to reduce running time and memory consumption.


CHANGES IN MALDIquant VERSION 1.4 [2012-10-30]:
-----------------------------------------------

NEW FEATURES

* Add slot "snr" to MassPeaks.
* Add `.estimateNoiseMad` (same implementation as old `estimateNoise` method).
* Add `.estimateNoiseSuperSmoother`.
* `estimateNoise`: add method argument, change return value to two column
  matrix.
* `binPeaks`/`referencePeaks`: add argument method=c("strict", "relaxed");
  "relaxed" allows multiple peaks of the same spectrum in a bin.

IMPROVEMENTS

* `labelPeaks`: remove tolerance argument (now always select the closest one).
* `mergeMassPeaks`/`mergeMassSpectra`: merge metaData, too.
* `detectPeaks`: new example for a custom noise estimation function.
* `calibrate`: add ... to generic definition of `calibrate`.
* Change demo licences to public domain.

INTERNAL CHANGES

* `detectPeaks`: change internal snr handling.
* `show`: rewrite (OO design).


CHANGES IN MALDIquant VERSION 1.3 [2012-09-16]:
-----------------------------------------------

NEW FEATURES

* Add `trim` and `[` methods.
* `labelPeaks`: add avoidOverlap argument to avoid overlapping of peak labels.

IMPROVEMENTS

* `detectPeaks`: add error message if windowSize >= length.
* `determineWarpingFunctions`: add error message if it could not match any peak
  to reference peaks.

MODIFICATIONS

* `labelPeaks`: change default value for verticalOffset argument.
* `labelPeaks`: remove family argument.

BUG FIXES

* Fix `isMassSpectrumList`.

GENERAL

* Update DESCRIPTION file to use Authors@R and depends on R>=2.14 now.
* Add CITATION file.


CHANGES IN MALDIquant VERSION 1.2 [2012-07-18]:
-----------------------------------------------

BUG FIXES

* `determineWarpingFunctions`: stop with an error if reference MassPeaks
  object is empty.
* `.doByLabel`: preserve list order (affects `filterPeaks`).

INTERNAL CHANGES

* Replace some `sapply` calls by `lapply`.


CHANGES IN MALDIquant VERSION 1.1 [2012-05-06]:
-----------------------------------------------

NEW FEATURES

* Add `totalIonCurrent` method (replacement for `calibrate` function on
  MassSpectrum objects).
* Add methods accepting lists as arguments: `transformIntensity`,
  `removeBaseline`, `detectPeaks`.

MODIFICATIONS

* `detectPeaks`: remove localMaxima argument.
* `detectPeaks`: replace noise argument by fun.
* `removeBaseline`: replace baseline argument by fun.
* `labelPeaks`: use par("usr") to calculate default verticalOffset.
* `labelPeaks`: add absoluteVerticalPos argument.
* `plot`: change "sub" for merged spectra/peaks.
* `intensityMatrix`: remove argument replaceByNa.
* `determineWarpingFunctions`, `warpMassSpectra`, `warpMassPeaks` now require
  lists as arguments and return a list.
* `calibrate`: works only on matrices now.
* Replace all `lapply` calls by new methods in demonstration scripts.
* Allow only numeric values for `intensity<-` and `mass<-`.
* Rename `findLocalMaxima` to `.findLocalMaxima` and hide by NAMESPACE.
* Rename dataset spectra in fiedler2009subset.
* Remove peaks dataset.


CHANGES IN MALDIquant VERSION 1.0 [2012-03-28]:
-----------------------------------------------

NEW FEATURES

* Add demonstration scripts.
* Add functions: `binPeaks`, `determineWarpingFunctions`, `filterPeaks`,
  `isMassObject`, `isMassPeaks`, `isMassSpectrum`, `mergeMassPeaks`,
  `mergeMassSpectra`, `referencePeaks`, `warpMassPeaks`, `warpMassSpectra`.

MODIFICATIONS

* Change NAMESPACE.
* Hide `imputeMass` method because it fails on Bruker Daltonics' CompassXport
  32bit output.
* Add \keyword{internal} to estimateBasline*-functions.Rd.
* `labelPeaks`: rename massTolerance argument to tolerance.
* Replace dataset sA1/pA1 by spectra/peaks (containing 16 example spectra).


CHANGES IN MALDIquant VERSION 0.5 [2012-01-18]:
-----------------------------------------------

NEW FEATURES

* Add `imputeMass` method.

IMPROVEMENTS

* Rewrite intensityMatrix function (little speed improvement).


CHANGES IN MALDIquant VERSION 0.4 [2011-08-04]:
-----------------------------------------------

NEW FEATURES

* Add functions: `isMassObjectList`, `isMassPeaksList`, `isMassSpectrumList`,
  `findEmptyMassObjects`, `removeEmptyMassObjects`, `intensityMatrix` and
  `calibrate` (only TIC supported up to now).
* Add mass and massTolerance argument to `labelPeaks`.

IMPROVEMENTS

* Change default value for verticalOffset argument in `labelPeaks`.
* Add pA1 dataset.

MODIFICATIONS

* Rename AbstractMassSpectrumData to AbstractMassObject.


CHANGES IN MALDIquant VERSION 0.3 [2011-05-28]:
-----------------------------------------------

NEW FEATURES

* Add `transformIntensity`, `estimateNoise`, `findLocalMaxima`, `detectPeaks`
  and `points` method.
* Add `createMassPeaks` constructor.

IMPROVEMENTS

* Replace `.estimateBaselineMovingEstimator` by `.estimateBaselineMedian` (uses
  `runmed` instead of an own slow `movingEstimator` function).

MODIFICATIONS

* Rewrite `labelPeaks` (some arguments changed).
* Rename SingleSpectrum class to MassSpectrum.
* Rename SinglePeakList class to MassPeaks.
* Remove fdrtool dependency and rewrite `.estimateBaselineConvexHull` in C.
* Move importing functions to the following R-packages: readBrukerFlexData,
  readMzXmlData.

BUG FIXES

* change `.C(..., DUP=F)` to `.C(..., DUP=T)` in `.estimateBaselineSnip`
  to avoid changes of global variables.


CHANGES IN MALDIquant VERSION 0.2 [2011-03-29]:
-----------------------------------------------

* Add baseline correction algorithm SNIP (implemented in C) [default].
* Add MovingEstimator and ConvexHull baseline estimation algorithm.
* Add `as.matrix`, `intensity`, `length`, `lines`, `mass` and `metaData`
  methods.
* Add basic SinglePeakList class, adopt `plot` and `lines`, add `labelPeaks`
  (still useless).


CHANGES IN MALDIquant VERSION 0.1 [2011-02-22]:
-----------------------------------------------

* First public release.
* Up to now only importing and plotting of a single mass spectrum are supported.