This file is indexed.

/usr/lib/R/site-library/gplots/NEWS is in r-cran-gplots 3.0.1-2.

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
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
Release 3.0.1 - 2016-03-30
--------------------------

Bug Fixes:

- An error in plotLowess() prevented it from finding objects in
	the caller's environment.

- The manual page for heatmap.2() stated the incorrect type for
  the 'layout' element of the return list.  It is a named list,
  not a named numeric vector.


Release 3.0.0 - 2016-03-28
---------------------------

New Features:

- venn():
    - now support matrices of indicator values. Previously indicator
      values were only supported when supplied as a dataframe.
    - The 'intersections' attribute returned from venn() has been
      improved so that goups are labeled using set names instead
      of indicators, and are ordered from simplest to most complex
      set intersection.

- New angleAxis() function to create axis labels with rotated text.

- heatmap.2():
    - heatmap.2() can now be used to plot subsets of a previous
      heatmap.
    - Decrease the granularity of the carpet in heatmap.2()'s
      color key to avoid visual artifacts.
    - Returned object now includes 'layout' element that contains
      layout information. (Patch provided by Jenny Drnevich.)

- lowess():
    - New function plotLowess() to display a scatter plot with a
      superimposed lowess curve.
    - The lowess() functions now returns a list object of class
      'lowess'
    - A new lowess method for plot() method for 'lowess' objects
      that generates a scatterplot of the raw data with a lowess
      curve superimposed.

Bug Fixes:

- Defunct message for boxplot.n() was recommending the wrong
  function.

- heatmap.2():
  - Remove debugging print() statement.
  - Now properly sets 'srtCol' default if missing and 'colCol' is
    specified.
  - Corrected a bug causing "Error in plot.new() : figure margins
    too large" to occur when 'key=FALSE'.  (Reported and patch
    provided by Sveinung Gundersen.)
  - Corrected a bug causing an error when "Rowv=FALSE" or "Colv=FALSE".
  - Corrected message when "Rowv=FALSE" or "Colv=FALSE" and the the
    "dendrogram" argument requested the corresponding dendrogram.

- venn():
  - Fix warning message that was missing spaces between words.

Other Changes:

- The smartlegend(), plot.lm2(), and boxplot.n() functions are now
  defunct. Please use grephics::legend(), lmplot2() or boxplot2()
  respectively.


Release 2.17.0 - 2015-05-01
---------------------------

New Features:

- heatmap.2() has two new arguments, 'colRow' and 'colCol' to control
  the color of row and column text labels. See the man page for
  examples.

- heatmap.2() has been modified to make it easier to extract and plot
  subclusters from a large heatmap. Simply pass the dendrogram of the
  subcluster together with the full data matrix and, optionally, the
  breaks of the full heatmap in order to obtain the same color
  scaling. (Suggestion and patch contributed by Ilia Kats.)

- venn() now returns a list of the members of each set intersection in
  the attribute 'intersections'.  This can be disabled using the
  argument 'intersection=FALSE' (Patch by Steffen Möller.)

Bug Fixes:

- In heatmap.2(), the color key now properly handles color breaks that
  are not equally spaced. (Issue reported by Tim Richter-Heitmann.)

- In heatmap.2(), row/column traces in could be plotted on the wrong
  row/column.

- plotCI() now properly respects the 'type=' argument.  (Bug report
  and correction by Wiktor Żelazny.)

- Remove stray browser() call from overplot()

- In the balloonplot() examples, explicitly specify the 'neworder'
  argument to gplots:::reorder.factor to prevent errors.

Other Changes:

- smartlegend() is now deprecated because the relative positioning
  feature ('top', 'right') has been added to graphics::legend().
  Calling smartlegend() will generate a warning.

- boxplot.n() and plot.lm2() are defunct have been removed.  Use of
  these functions will now generate an error.

- Update out-of-date URLs in man pages.

Release 2.16.0 - 2015-01-02
---------------------------

New Features:

- plotmeans() has a new argument, 'text.n.label' which specifies the
  text used for labeling the number of elements in a group.

Bug Fixes:

- plotmeans() now respects (optional) graphical arguments captured in
  '...' when drawing the x axis.


Release 2.15.0 - 2014-12-01
---------------------------

New features:

- Convert bandplot() to S3-method dispatch and add method for class
  formula, so that 'bandplot( y ~ x, data=dataframe )' now works as
  expected.

Other changes:

- heatmap.2() now uses a local *non-byte-compiled* copy of
  plot.dengrogram, because the byte-compiled stats:::plot.dendrogram
  uses a recursive algorithm that generates a 'node stack overflow'
  error for deeply nested dendrograms and the node stack size cannot
  be changed at execution time.  Instead, tne local non-byte-compiled
  gplots:::plot.dendrogram will trigger a recursion limit for such
  dengrograms.  heatmap.2() will detect this error and recommend that
  the user increase the recursion limit (via,
  e.g. 'options("expressions"=20000)' ) and rerun.

Release 2.14.2 - 2014-09-17
---------------------------

Bug Fixes:

- heatmap.2() was not respecting key.title=NA when density.info="none".

- Correct the man page for heatmap.2 to state that the default color
  for 'notecol' is cyan.

- In heatmap.2(), modify default arguments to 'symbreaks' and 'symkey'
  to make the logic more evident by replacing min(...) with
  any(...). (The previous code executed properly, but relied on
  implicit coercion of logicals to numeric, obscuring the intent.)

- Calling heatmap.2 with deeply nested dendrograms could trigger a
  'node stack overflow' error.  Now, this situation is deteceted, and
  a message is generated indicating how to increase the relevant
  recursion limit via options("expressions"=...).

Release 2.14.1 - 2014-06-30
---------------------------

Bug Fixes:

- Correct heatmap.2() bug in Colv dendrogram object dimension checking introduced
  in 2.14.0.  (Reported by Yong Fuga Li.)


Release 2.14.0 - 2014-06-18
---------------------------

Bug Fixes:

- heatmap.2(): Fix typo in heatmap.2() that caused an error when
  'Rowv=FALSE'. (Reported by Yuanhua Liu.)

Enhancements:

- heatmap.2(): Add new 'reorderfun' argument to allow the user to
  specify an alternative function to reorder rows/columns based on
  row/column dendrogram. (Suggested by Yuanhua Liu.)

- heatmap.2(): Center margin labels.

- heatmap.2(): Check size of user-provided Rowv and Colv dendrogram
  objects to ensure they match the dimensions of the data.

- Add references to man page for hist2d() and ci2d() to the new r2d2
  package which implements an improved algorithm for 2-dimensional
  emprical confidence regions.


Release 2.13.0 - 2014-04-04
---------------------------

Bug Fixes:

- heatmap.2 was not properly handling row trace reference line ('hline').
  Patch submitted by Ilia Kats.

Enhancements:

- In heatmap.2, when the row or column trace is enabled, show the
  corresponding reference line in the color key.

- In heatmap.2, a new 'extrafun' argument is provided that allows the
  user to specify a function to be called before the function returns.
  This allows the user to add additional plots to the page.


Release 2.12.1 - 2013-10-14
---------------------------

API Changes:

- boxplot.n() has been renamed to boxplot2() to avoid potential S3
  method calling issues.

- plot.lm2() has been rename to lmplot2() to avoid potential S3 method
  calling issues.

Enhancements:

- Add heatmap.2() parameters to control row and column label rotation
  ('srtRow', 'srtCol'), justification ('adjRow', 'adjCol'), and space
  from plot edge ('offsetRow', 'offsetCol').

Bug Fixes:

- Fix error in in venn() when all groups contained the same number of TRUE cases.

- Correct error in overplot() when that occured when a group-category contained no
  finite values.

Other Changes:

- Changes to overplot() to avoid warnings from upcoming enhancements to R CMD check.

- Move several packages from Depends to Imports or Suggests.

- Packages caTools and KernSmooth now have namespaces, so import
  needed functions in NAMESPACE.

- Mark one example in manual page for ci2d 'dontrun' to avoid timing
  warning in R CMD check.


Release 2.11.3 - 2013-06-27
---------------------------

Enhancements:

- Modify sinkplot() to use a local environment rather than the global
  environment, to conform to CRAN policies.

Bug Fixes:

- Fixed typo/spelling error in plotmeans() man page.


Release 2.11.2 - 2013-03-24
---------------------------

Enhancements:

- Add ci.width argument to barplot2() to allow varying the length of
  the 't' at the end of confidence interval bars.

Bug Fixes:

- Fix error in heatmap.2 when colsep argument had length 1.

Updates:

- Update manual page for lowess.default() to
  match changed argument list for lowess() in R 3.0.0


Release 2.11.1 - 2012-12-14
---------------------------

Bug Fixes:

- Replace corrupted BalloonPlot.pdf in inst/doc.


Release 2.11.0 - 2012-06-08
---------------------------

New Features:

- Objects returned by hist2d() have been changed:
  1) $x and $y now contain the n midpoints of the bins in each direction
  2) $x.breaks, $y.breaks now contain the n+1 limits of the bins in
  each direction.

- Add lwd argument to plotmeans().

Bug Fixes:

- Correct error in handling binning in hist2d(): (N+1)x(N+1) bins were
   being created instead of NxN bins, and the highest row/column in
   each direction was being omitted from the results and plot.

- Changes to fix R CMD check warnings


Release 2.10.1 - 2011-09-02
---------------------------

New features:

- Make results of hist2d() and ci2d() into objects, and add print()
  methods to display them.

Release 2.10.0 - 2011-08-26
---------------------------

New Features:

- New ci2d() function to create 2-dimensional empirical confidence
  intervals utilizing KernSmooth:bkde2D and gplots::hist2d().
  See ?ci2d for details.

- Add 'alpha' argument to rich.colors() to control transparency.

Improvements:

- Accellerate hist2d by replacing for() loop with tapply(), and allow
  user to specify summary function applied (per suggestion by Peter
  Hagedorn).

Bug Fixes:

- Correct error in heatmap.2() that arises when data includes NA values
  (identified by Melissa Key).


Release 2.8.0 - 2010-06-10
--------------------------

Improvements:

- venn() now returns an object of class venn() and a plot method for
  this class is provided.

- Manual page for venn has been improved, based on contributions by
  Steffen Moeller


Release 2.7.5 - ??
--------------------------

Improvements:

- Performance of 'hist2d' improved thanks to a suggestion from
  Joerg van den Hoff.

Release 2.7.4 - 2009-11-12
--------------------------

Bug Fixes:

- Correct bug reported by Alan Yong:  plotmeans() failed when bars=FALSE.

Release 2.7.3 - 2009-10-22
--------------------------

Bug Fixes:

- Correct bug reported by Rudolf Talens: heatmap.2() incorrectly
  transposed the displayed matrix when the option symm=TRUE.


Release 2.7.2 - 2009-05-08
--------------------------

Bug Fixes:

- Correct bug reported by Ken Lo:  cox2hex() had blue and green
  components swapped.


Release 2.7.1 - 2009-05-08
--------------------------

New Features:


- Enhancements to heatmap.2()

    - New arguments 'lmat', 'lhei', and 'lwid' that allow controlling
      component plot layout.  Users can now resize and rearrange plot
      components.

    - heatmap.2() will now compute color breakpoints that are
      symmetric about 0 when the new 'symbreak' parameter is TRUE.  This
      parameter, as well as the symkey parameter now default to TRUE
      whenever negative values of x are present, and to FALSE othewise.

    - the heatmap.2() return value now includes additional useful
      information, including: call, rowMeans, rowSDs, colMeans,
      colSDs, carpet (reordered and scaled 'x' values), rowDendrogram,
      colDendrogram, breaks, col, vline, hline, and colorTable. Of
      these, the most useful are breaks, col, and colorTable.  The
      latter is a three-column data frame providing the lower and
      upper bound and color for each bin.

  See the manual page for complete details and examples.


- New function venn(), contributed by Steffen Moeller (Thanks
  Steffen!) to generate Venn diagrams for up to 5 sets. See ?venn for
  details.

- Performance of bandplot() has been dramatically improved, in part by
  using runsd() and runmean() from the caTools package.  As a
  consequence, gplots now depends on the caTools package.

- Improved performance of gplots::plot.lm for large lm objects by
  using the new bandplot() and by using fitted() instead of predict()
  to obtain y-hat.

- Add 'scale.range' argument to balloonplot(), option to scale
  balloons so [min,max]->[0,1] ('relative') or [0,max] -> [0,1]
  ('absolute').


Bug Fixes:

- balloonplot() now properly handles dimension labels provided by
  'xlab' and 'ylab'

- plotCI now properly handles 'NULL' and 'NA' values for ui, li, uiw,
  and liw.

- Corrections of minor typos in man pages

- Update Greg's email address to 'greg@random-technologies-llc.com'


Release 2.6.0 - 2008-04-07
--------------------------

New Features:

- heatmap() now allows control of the location of individual plot components
   (e.g. color key)

Bug Fixes:

- Fix bug in handling rowsep, per suggestion by Steven Paugh

- Fix examples for overplot()

- Two letter clarification of help text for heatmap.2()

- Restore plot layout settings to default state at end of ooplot() example

- Various typo fixes

Release 2.5.0 - 2007-11-02
--------------------------

New Features:

- textplot() now converts tab characters to spaces before processing to
  avoid problems with computing height and width of text that includes
  tabs.

- Add col2hex() function to convert color names to rgb hex codes

Bug Fixes:

- Correct balloonplot.default to properly show specified x and y axis
  labels when explicitly provided

- R/balloonplot.R: Correct error in balloonplot when z contains NA values.

- Fix typos and code/doc mismatches identified by the latest R CMD check

Other:

- Clarify GPL version

Release 2.4.0 - 2007-02-08
--------------------------

New Features:

- Add parameters to bandplot() to control line width and type.

- Add paramaeters to textplot.matrix() to allow specification of the
   color of the matrix data, rows, and column

Bug Fixes:


Other:


Release 2.3.2 - 2006-11-14
--------------------------

- heatmap.2.Rd: Fix example that was broken by changes in 2.3.0.


Release 2.3.1
-------------

- Changed maintainer back to Greg Warnes

- Updated Greg's email address

- heatmap.2.R: Fixed a bug which displayed warnings when Rowv and Colv
  were specified as dendrograms


Release 2.3.0
-------------

 - heatmap.2.R, heatmap.2.Rd:

          Updated the code and man page to make sure the Rowv and Colv
          values are properly handled

 - Added the tests directory



Release 2.2.0
-------------

 - plotmeans.R: Fixed bug in plotmeans - based on Stefano Calza's
	        suggestion (the function didn't account for factors
		unused levels, returning an error.)

 - exported plot.lm to NAMESPACE, Remove .Alias calls in plot.lm.R
 		since .Alias is defunct.

 - barplot2.R: Changed the default grey colors to heat colors, if
	       height is matrix

 - Updated Greg's email address

 - balloonplot.R: Recent changes to align row totals with the
	  	  overall total broke how the marginal cumulative
	  	  fractions were displayed. Added example using
	  	  Titanic data that exercises the multi-factor display.
 		  Added -.tex, .pdf files and figuers, and RNEWS article
		  in inst/doc

 - colorpanel.R: colorpanel now allows only 2 colors to be specified
		 if no 'middle' color is desired.


Release 2.0.8
-------------

 - Added DESCRIPTION and removed DESCRIPTION.in

 - Updated barplot2

 - Updated heatmap.2