-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathNEWS
2834 lines (1617 loc) · 84.3 KB
/
NEWS
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
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
Package: R.utils
================
Version: 2.11.0 [2021-09-25]
NEW FEATURES:
* Now insert() support duplicates in 'ats', which then results in the
corresponding 'values' being inserted in order at those duplicated indices.
* Relaxed insert() to accept a 'values' argument that is a list but not
necessarily a formal vector.
* Now queryRCmdCheck() sets environment variable R_CMD_CHECK=true if it
detects 'R CMD check' is running.
* Added format() for 'binmode'.
* hpaste() gained argument 'empty', which can be used to control what to
return in case the output is of length zero.
BUG FIXES:
* gcDLLs() produced a "In sprintf(...) : argument not used by format" warning
when giving an error message on what DLLs it failed to unload.
* Arguments$getVector() could produce an error on "argument is missing, with
no default" while trying to signal an assertion error.
* intToHex() and intToOct() would no longer pad with zero on recent R-devel
(to become R 4.2.0) versions.
Version: 2.10.1 [2020-08-25]
NEW FEATURES:
* Updated legacy function useRepos() to use HTTPS instead of HTTP.
DOCUMENTATION:
* Update URLs with 301 redirects. Most of them were HTTP to HTTPS redirects.
Version: 2.10.0 [2020-08-24]
NEW FEATURES:
* R.utils::commandArgs() recognizes new '--no-echo' option in R (>= 4.0.0).
BUG FIXES:
* R.utils::getAbsolutePath("~/../Documents", expandTilde = TRUE) would adjust
for '..' before adjusting for '~' resulting in an incorrect path. Thanks
to Dean Attali for reporting on this.
Version: 2.9.2 [2019-12-07]
* CRAN POLICY CRAN: The help example for FileProgressBar and its package
tests wrote to the user's home directory. They are now writing to a
temporary directory instead.
Version: 2.9.1 [2019-12-05]
BUG FIXES:
* wrap() for arrays used a list - not a numeric vector - to assign dimensions.
This would produce an error in R (>= 4.0.0).
* withSeed(..., seed = NULL) did not work for R (< 3.0.0).
* fileAccess(..., mode = 2) would update .Random.seed.
* fileAccess(path, mode = 2) could end up in an end less loop if the 'path'
folder contained all files of 'a, b, ..., z, A, B, ... Z'.
Version: 2.9.0 [2019-06-11]
BUG FIXES:
* sourceDirectory() did not respect argument 'modifiedOnly'. Thanks to
Anton Krasikov for the report and the fix.
* createLink() could produce a spurious warning on MS Windows.
DEPRECATE AND DEFUNCT:
* Previously defunct arrayIndex(), evalWithTimeout(), and resetWarnings()
have been removed.
* Assert$inherits() is defunct - use Assert$inheritsFrom() instead.
* Argument 'substitute' of withCapture() is defunct - use 'replace' instead.
Version: 2.8.0 [2019-02-13]
NEW FEATURES:
* createWindowsShortcut() gained argument 'mustWork'.
* When createLink() fails, the error message now also report on the methods
attempted.
BUG FIXES:
* displayCode(), commandArgs() and toCamelCase() used && and || on logical
vectors that might not necessarily be of length one.
* createWindowsShortcut() and createLink(method="windows-shortcut") failed to
create Windows Shortcut links because filePath(..., expandLinks = "any")
did not expand Windows Shortcut links. This bug was introduced in
R.utils 1.34.0 (2014-10-07) due to a cut'n'paste mistake.
Version: 2.7.0 [2018-08-26]
NEW FEATURES:
* Added nullcon() that returns a (binary) connection to the nullfile().
PERFORMANCE:
* readTable() no longer runs the garbage collector - was done so implicitly
through an internal system.time() call without using gcFirst = FALSE.
BUG FIXES:
* Rscript -e "R.utils::cmdArg(a=42L)" -a:=1:3 would set 'a' to NA_integer_.
DEPRECATE AND DEFUNCT:
* evalWithTimeout() is now defunct. Use withTimeout() instead.
* arrayIndex() is now defunct. Use base::arrayInd() instead.
* Assert$inherits() is deprecated - renamed to Assert$inheritsFrom().
* Removed deprecated and ignored argument 'reset' of warnings() for Verbose.
Version: 2.6.0 [2017-11-05]
NEW FEATURES:
* Argument 'install' of use() now defaults to option 'R.utils.use.install',
which in turn defaults to environment variable 'R_R_UTILS_USE_INSTALL'.
If neither is set, the default is TRUE.
* ROBUSTNESS: Now gcDLLs() runs the garbage collector before removing stray
DLLs in order for any finalizers who rely on the DLL to be called before the
DLL is removed.
* loadObject() and loadToEnv() give more informative error message if an
error occurs while reading from a file / connection.
* All withNnn() functions gained argument 'substitute' making it possible to
pass an expression object, e.g. withTimeout(expr, subsitute = FALSE, ...).
The exception is withCapture(), where, the now deprecated (see below),
argument 'substitute' means something else for legacy reasons.
BUG FIXES:
* withTimeout() would produce a regular error but not a TimeoutException
for timeouts reaching the _total_ CPU time limit while it would work
for those reaching the _elapsed_ CPU time limit. Thanks to Alexej Gossmann
at Tulane University for troubleshooting and provide a fix.
* findSourceTraceback() could fail and give an obscure error when for instance
the 'XML' package was attached. It now tries a bit harder to locate the
internal 'srcfile' object.
* Forgot to register S3 method `[`() for GenericSummary.
* intToOct() would convert to hexadecimals.
* intToBin() would output garbage for negative values.
DEPRECATE AND DEFUNCT:
* Argument 'substitute' of withCapture() has been renamed to 'replace'.
Code that calls withCapture(..., substitute = ...) will still work, but
the use of 'substitute' is deprecated and will later become defunct.
The purpose of this change of argument name is so that the meaning of
'substitute' can be harmonized with the other withNnn() functions.
* Deprecated evalWithTimeout(); use withTimeout() - the preferred name.
Version: 2.5.0 [2016-11-07]
BUG FIXES:
* withCapture(x <- 1L) would drop integer suffix 'L' from the output when run
in non-interactive mode.
DEPRECATE AND DEFUNCT:
* CLEANUP: Removed operator `%<-%` which was defunct since 2.4.0.
An alternative is to use ditto of the future package.
* CLEANUP: Made resetWarnings() defunct.
Version: 2.4.0 [2016-09-13]
NEW FEATURES:
* Added strayDLLs() and gcDLLs() to identify and unload stray DLLs that was
left behind by packages that have already been unloaded.
* Added nullfile().
* Now setThreshold() for Verbose accepts also logical values.
* Argument 'absolutePath' for Arguments$getReadablePathname() was renamed to
'absolute'. For backward compatibililty, the old name will still work for
some time.
DEPRECATE AND DEFUNCT:
* CLEANUP: Defunct `%<-%` in favor of `%<-%` in the future package.
* CLEANUP: Deprecated arrayIndex(). arrayInd() in base (>= 2.11.0)
provides the same functionality.
CODE REFACTORING:
* Package now formally requires R (>= 2.14.0) released October 2011.
Version: 2.3.0 [2016-04-13]
NEW FEATURES:
* Added hsize().
* Added tmpfile() for creating temporary files with content that is deleted
automatically by the garbage collector unless there is a reference to it.
* ROBUSTNESS: Now compressFile() and decompressFile(), and therefore also
functions such as gzip() and gunzip(), output atomically by writing to a
temporary file which is only renamed when completed.
DEPRECATE AND DEFUNCT:
* CLEANUP: Deprecated `%<-%` in favor of `%<-%` in the future package.
CODE REFACTORING:
* Package now formally requires R (>= 2.14.0) released Oct 2011.
Version: 2.2.0 [2015-12-09]
NEW FEATURES:
* loadObject() and saveObject() gained argument 'format' in order to support
also RDS files (in addition to XDR files). File formats XDR and RDS are
supported. The default format is inferred from the filename extension. If
this is not possible, then the XDR format is assumed (default; backward
compatible).
* mkdirs() gained arguments 'mustWork' and 'maxTries'.
* seqToHumanReadable() gained argument 'tau'.
* R.utils::commandArgs() now also ackowledges 'argv' set by the littler
executable.
* R.utils::commandArgs() recognizes more reserved command-line arguments, e.g.
--debugger-args=N, --min-vsize=N and --min-nsize=N.
* ROBUSTNESS: Now writeDataFrame(..., sep, quote = FALSE) asserts that none of
the columns contains the field separator 'sep', because then the written
file would be corrupt/invalid.
* ROBUSTNESS: Explicit import of all 'graphics', 'grDevices', 'stats' and
'utils' functions.
DOCUMENTATION:
* Clarified in help for compressFile() et al. that these functions remove the
input file by default after the output file is generated. Thanks to Ben
Bond-Lamberty (Pacific Northwest National Laboratory) for pointing out this
potential pitfall.
BUG FIXES:
* seqToHumanReadable(c(1:2, 4:5)) gave "1-2, 4, 5".
* withTimeout() did not work in non-English locales. Thanks to Arnaud Malapert
at University Nice Sophia Antipolis for reporting on this.
* GString ignored "simple" attributes, e.g. $[tolower]{y}. Thanks to Andre
Mikulec for reporting on this.
* downloadFile() via https://<user>:<pwd>@<domain>/ gave an error.
DEPRECATE AND DEFUNCT:
* CLEANUP: Deprecated resetWarnings().
Version: 2.1.0 [2015-05-27]
NEW FEATURES:
* Added compressPDF() to compress PDFs.
* If, and only if, 'path' is an existing directory, then copyFile(pathname,
path) copies file 'pathname' to the 'path' directory (previously destination
always had to be a file). Analogously, renameFile(pathname, path) moves file
'pathname' (not a directory though) to destination directory 'path'.
* CLEANUP: createLink(..., skip = TRUE) would give a false warning if a proper
link already existed and the target was elsewhere than the current directory.
* INCONSISTENCY: captureOutput(..., collapse = "\n") did not drop newline of the
last line as captureOutput(..., collapse = "\r") and any other collapse != "\n"
strings. Added package tests.
BUG FIXES:
* captureOutput(..., file = "foo.txt") gave an error.
Version: 2.0.2 [2015-04-27]
BUG FIXES:
* Arguments$getReadablePathname(NA, mustExist = FALSE) no longer gives an error
with recent R devel (>= 2015-04-23) related to an update on how nchar()
handles missing values. This bug affected only Windows.
CODE REFACTORING:
* ROBUSTNESS: Now nchar(..., type = "chars") is used internally for all file and
directory names.
Version: 2.0.1 [2015-04-24]
NEW FEATURES:
* R.utils no longer generates a warning if the R session is saved when R
exits. Thanks to Jose Alquicira Hernandez for reporting on this.
BUG FIXES:
* toCamelCase() with missing values would give an error in R devel
(>= 2015-04-23) due to an update how nchar() handles missing values.
Version: 2.0.0 [2015-02-28]
NEW FEATURES:
* ROBUSTNESS: Now %<-% evaluates the expression in a local() environment, and
it assign to environments, e.g. env$a %<-% 1.
* Added compressFile(), decompressFile() and isCompressedFile() methods, which
gzip()/gunzip() and the new bzip2()/bunzip2() now use. Thanks to Peter
Hickey for pushing for this.
* Now eget() uses inherits = FALSE (was TRUE) and mode = "default" (was
"any"), where "default" corresponds to the mode of argument 'default',
unless it's NULL when mode = "any" is used.
* Now commandArgs(asValues = TRUE, adhoc = TRUE) interprets 'x:=1:10' such that 'x'
become the integer vector 1:10. Likewise, you can do 'x:=seq(1,3, by = 0.1)'
and 'x:=pi'. To get the string "pi", use quotation marks, i.e. 'x:="pi"',
or just 'x=pi'.
* Added cmsg(), cout(), ccat(), cprintf(), cprint(), cstr(), cshow() for
outputting to "console", which is neither R stdout nor stderr and can
therefor not be intercepted via capture.output(), sink() or similar. These
functions are useful for outputting messages that requires user's attention
and are often followed by a prompt via readline(), which also cannot be
captured.
* Added mpager() which is a "pager" function compatible with file.show() that
will display file contents on standard error.
* Just like for listDirectory(), argument 'recursive' of findFiles() can in
addition to be FALSE (depth = 0) and TRUE (depth = +Inf), be any non-negative
numeric number specifying how deeply the recursive search should be done.
* On Windows, Arguments$getReadablePathname() now gives an informative warning
if a pathname of length 256 or longer is used/generated, which are not
supported on Windows.
DOCUMENTATION:
* Fixed mistake in help("captureOutput"). Thanks to Mikko Korpela (Issue #4)
for reporting on this.
BUG FIXES:
* use(..., quietly = FALSE) no longer captures/buffers the output, which
prevented it from displaying full prompt messages that required a user
response. use(..., quietly = TRUE), which is the default, no longer tries to
ask user of Windows and OS X if they wish to install from source if the
binary is older.
* Now the returned value of all withNnn() functions preserves the "visibility"
of the eval():uated expression. Added package tests.
* withCapture({}) no longer generates a warning.
* Now isUrl(NA) returns FALSE (instead of NA).
* seqToIntervals(integer(0)) gave error "object 'res' not found".
* attachLocally() on an environment would remove the attached fields/variables
from that environment.
CODE REFACTORING:
* ROBUSTNESS: Forgot to declare "default" warnings() as an S3 method.
* R.utils::use() without arguments attaches 'R.utils'.
* ROBUSTNESS: Package test coverage is 66%.
Version: 1.34.0 [2014-10-07]
CODE REFACTORING:
* Added URL and BugReports fields to DESCRIPTION.
* Submitted to CRAN.
Version: 1.33.10 [2014-10-03]
NEW FEATURES:
* Added shell.exec2(), which does a better job than shell.exec() in opening
pathnames with forward slashes and files on mapped drives, which may or may
not open depending software, e.g. Google Chrome fails to open the latter.
Add options(browser = function(...) R.utils::shell.exec2(...)) to your
~/.Rprofile file to make browseURL() use this function instead of
shell.exec(). This function is only useful on Windows.
BUG FIXES:
* Now Arguments$getReadablePathname(file, path) ignores 'path' if 'file'
specifies an absolute pathname.
Version: 1.33.9 [2014-10-03]
NEW FEATURES:
* Now countLines() automatically supports gzipped files as well. Thanks to
Sarah Nelson at Dept of Biostatistics at University of Washington for the
suggestion.
* Now downloadFile("https://...") will use 'curl', and if not available 'wget',
to download the file over the HTTPS protocol. Previously only 'wget' was
used. The 'curl' software is available on more operating systems, include
OS X, whereas 'wget' sometimes needs a separate installation.
Version: 1.33.8 [2014-10-02]
NEW FEATURES:
* Added argument 'unmap' to filePath() for "following" paths that are on
mapped Windows drives.
* CLEANUP: use() would try temporarily set package repository options even
when not needed. This could trigger unnecessary warnings for users who
haven't set a default CRAN mirror and using use() to load/attach an already
installed package.
Version: 1.33.7 [2014-09-18]
NEW FEATURES:
* New default for writeDataFrame() - argument 'col.names = !append'. Also, if
append = TRUE, header comments are only written if specified. Added package
system test for writeDataFrame().
Version: 1.33.6 [2014-09-16]
BUG FIXES:
* getAbsolutePath("/tmp", expandTilde = TRUE) returned "//tmp". This would in
turn have implications on getRelativePath(), e.g. getRelativePath("/tmp/a",
relativeTo = "/tmp") returned "../../tmp/a".
Version: 1.33.5 [2014-09-15]
NEW FEATURES:
* Added withSeed() and withSink().
* ROBUSTNESS: Now withOptions() also resets all the options available upon
entry even if no explicit options were specified. This covers the case when
'expr' changes the options and/or adds new options, e.g.
withOptions({ options(width = 10, foo = "new"); str(letter) }).
Version: 1.33.4 [2014-09-05]
BUG FIXES:
* ROBUSTNESS: Arguments$getWritablePathname() could sometimes generate warning
"file.remove(pathnameT) : cannot remove file 'file...', reason 'Permission
denied'. Now it tries to remove that files several times before giving up.
Version: 1.33.3 [2014-09-04]
NEW FEATURES:
* ROBUSTNESS: Now copyDirectory(), just as copyFile() already did, silently
drops arguments 'copy.mode' and 'copy.date' for older R versions where
base::file.copy() does not support them.
Version: 1.33.2 [2014-09-01]
BUG FIXES:
* mkdirs() could return "object 'res' not found" error.
Version: 1.33.1 [2014-08-25]
BUG FIXES:
* countLines() would not count the last line if it did not contain a newline.
It would also give an error if the newline characters were only CR. This
despite it was documented that both cases were supported. Added package
system tests for them.
Version: 1.33.0 [2014-08-24]
NEW FEATURES:
* Added mprint(), mcat(), mstr(), mshow() and mprintf() that work like the
corresponding print(), cat(), etc., but output using message(), which in
turn sends to standard error (instead of standard output). See also mout().
* Added withLocale().
* Now the test for target discrepancies by createLink(..., skip = TRUE) is
more forgiving on Windows (by assuming a case-insensitive file system)
before generating a warning.
* Now useRepos(..., fallback = TRUE), and hence use(), will fallback to
known/predefined CRAN repositories in case '@CRAN@' is not set. If done, it
will give an informative warning message.
BUG FIXES:
* commandArgs() would drop command-line arguments with periods, hyphens, or
underscores in their names, e.g. --src_file=x.
Version: 1.32.6 [2014-08-12]
BUG FIXES:
* withCapture({ if (T) 1 else 2 }) would give a parse error on "unexpected
'else'", because the internal deparsing puts the 'else' statement on a new
line whenever an if-else statement is enclosed in an { ... } expression.
This problem is also described in R help thread "deparse() and the 'else'
statement" by Yihui Xie on 2009-11-09
[http://tolstoy.newcastle.edu.au/R/e8/help/09/11/4204.html]. The workaround
is to detect standalone 'else' statements and merge them with the previous
line. Added package system test for this case.
Version: 1.32.5 [2014-05-15]
BUG FIXES:
* egsub() would return an invalid expression if the input had definitions of
functions without arguments, e.g. egsub("x", "x", substitute(y <-
function() 0)) which would throw "Error: badly formed function expression"
if deparsed/printed. Added package test for this.
Version: 1.32.4 [2014-05-14]
NEW FEATURES:
* Now egsub() also works with functions, in case it substitutes on the body of
the function.
DOCUMENTATION:
* Added clarification to help("withTimeout") on the limitations of the
function and when it is/is not possible to interrupt a function via timeouts.
SOFTWARE QUALITY:
* Made the package test on absolute and relative paths less conservative,
because it gave an error on Windows systems that have set R_USER to a
Cygwin-flavored directory, which causes normalizePath("~") to return a
non-existing directory. Thanks Uwe Ligges (CRAN) for reporting on this.
Version: 1.32.3 [2014-05-08]
BUG FIXES:
* filePath("./././././") now returns "." (was ""). Added package system tests
for filePath().
Version: 1.32.2 [2014-05-07]
NEW FEATURES:
* Added support for substitution of expressions in withCapture() based on
regular expressions utilizing new egsub().
* Added egsub(), which is gsub() for expressions with some bells and whistles.
Version: 1.32.1 [2014-05-04]
NEW FEATURES:
* Now downloadFile() "adjusts" the output filename by decoding URL encoded
characters, e.g. 'Hello%20world.txt' becomes 'Hello world.txt'. Also,
unsafe filename characters (':', '*', '\') are encoded, e.g.
'How_to:_RSP.txt' becomes 'How_to%3A_RSP.txt'.
* Added argument 'adjust' to Arguments$getReadablePathname(). When adjust =
"url" it decodes and encodes the filename the same way as downloadFile()
now adjusts it (see above).
Version: 1.32.0 [2014-05-01]
NEW FEATURES:
* Added captureOutput() which is much faster than capture.output() for large
outputs. withCapture() utilizes this now. Added package system tests for
both functions.
* use() now installs missing packages from all set repositories (as before)
and uses the mainstream (CRAN and BioC) ones as fall backs.
* Added withRepos() for installing/updating packages using a set of
temporarily set repositories. It is possible to specify repositories by
names, which are then selected from a set of known repositories, e.g.
withRepos(install.packages("edgeR"), repos = "[[BioC]]").
* Added withOptions() for evaluating an expression with a set of options
temporarily set.
* Renamed evalCapture() to withCapture() and evalWithTimeout() and
withTimeout(). The old name is kept for backward compatibility, but will
eventually be deprecated.
Version: 1.31.1 [2014-04-29]
NEW FEATURES:
* Now use("<repos>::<pkg>") will detect when a repository is unknown and give
an informative error message on how to update option 'repos'.
Version: 1.31.0 [2014-04-26]
NEW FEATURES:
* Added assignment operator %<-% for delayed assignments.
* Added option "evalCapture/newline".
Version: 1.30.7 [2014-04-26]
NEW FEATURES:
* Added argument 'xtrim' to draw() for density object.
* CLEANUP: createLink(..., skip = TRUE) no longer warns if the link file was
skipped. Now it only warns if the skipped link file links to a different
file than the intended target file.
CODE REFACTORING:
* CLEANUP: Dropping '::' in calls where possible.
Version: 1.30.6 [2014-04-24]
NEW FEATURES:
* Added argument 'newline' to evalCapture().
Version: 1.30.5 [2014-04-22]
NEW FEATURES:
* Added argument 'substitute' to evalCapture() for substituting symbols "on
the fly" in the expression before it is evaluated.
Version: 1.30.4 [2014-04-18]
NEW FEATURES:
* Added argument 'modifiedOnly' to sourceDirectory(), which was previously
passed via '...' to sourceTo(), and it now defaults to TRUE.
Version: 1.30.3 [2014-04-15]
BUG FIXES:
* use() would not install package dependencies.
Version: 1.30.2 [2014-04-08]
NEW FEATURES:
* Added argument 'max.deparse.length' to evalCapture().
Version: 1.30.1 [2014-04-06]
NEW FEATURES:
* Now evalCapture() utilizes deparse() to get the source code and acknowledges
options 'deparse.cutoff' to control the code wrapping. Previously
capture.output(print()) was used.
BUG FIXES:
* WORKAROUND: moveInSearchPath() redirects any messages to stderr that
base::attach() sent to stdout. UPDATE: This attach() issue has been fixed
in R 3.1.0 patched.
Version: 1.30.0 [2014-04-06]
NEW FEATURES:
* Vectorized detachPackage(), getAbsolutePath(), getRelativePath(),
isAbsolutePath(), isDirectory(), isFile(), isOpen(), isPackageInstalled(),
touchFile() and toUrl(). Added package system tests for several of them.
For backward compatibility, getAbsolutePath(), getRelativePath(),
isAbsolutePath(), isFile(), and isDirectory() treats an empty vector of
path/pathnames equal to ".". However, in a future version, empty results
will returned by these too.
BUG FIXES:
* toCamelCase(character(0L)) gave an error.
Version: 1.29.11 [2014-04-02]
BUG FIXES:
* str() and summary() for Verbose did not acknowledge argument 'level'.
Version: 1.29.10 [2014-02-28]
DOCUMENTATION:
* Added a help section on privileges required on Windows in order for
createLink() to work.
Version: 1.29.9 [2014-02-24]
NEW FEATURES:
* ROBUSTNESS: Added a package redundancy test for a bug occurring in R.oo
(< 1.18.0) causing R to core dump (with "Error: SET_VECTOR_ELT() can only be
applied to a 'list', not a 'integer'") or gives an error (with "Error: not a
weak reference") under certain conditions when a registered finalizer tried
to reload R.oo if it was unloaded. This occurred only on R prior to R 3.0.2
patched (2014-02-21 r65057). Also, the 'methods' package needs to be
attached, so it is still not clear what is the true cause of the bug. In
R.oo (>= 1.18.0) this bug is avoided.
Version: 1.29.8 [2014-01-27]
BUG FIXES:
* Although eget(K = 2, cmdArgs = TRUE) would use command-line argument 'K=1'
as the default (instead of K=2), calling eget("K", 2, cmdArgs = TRUE) would
not.
* commandArgs(excludeReserved = TRUE) failed to drop reserved arguments of
type --<key>=<value>, e.g. --encoding=ASCII.
Version: 1.29.7 [2014-01-27]
NEW FEATURES:
* Added trial version of the CmdArgsFunction class.
Version: 1.29.6 [2014-01-27]
NEW FEATURES:
* Added cmdArgsCall() for easy calling of functions from the command line,
e.g. Rscript -e R.utils::cmdArgsCall(rnorm) n=4.
Version: 1.29.5 [2014-01-27]
NEW FEATURES:
* doCall() gained argument 'envir', which also means that the new behavior is
to evaluate the call within the calling frame. Also, doCall() now accepts
call a function object in addition to a name of a function.
Version: 1.29.4 [2014-01-26]
NEW FEATURES:
* Added argument 'unique' to cmdArgs().
* Now commandArgs(asValues = TRUE) returns no-named arguments as a list
element with the argument as the value and with a "" name. For instance, in
the past one would get list(R = NA, a = "1", noname = NA) whereas now one
gets list("R", a = "1", "noname").
BUG FIXES:
* Now attachLocally() no longer tries to attach elements with an empty name,
e.g. list(a = 1, 2). Previously it gave an error. Added a package system
test for attachLocally().
Version: 1.29.3 [2014-01-19]
NEW FEATURES:
* CONSISTENCY: Now createLink(..., method = "windows-shortcut") returns the
path/pathname to the link (and not the target) just like it does for the
other types of file links. By link we here mean the path/pathname without
the *.lnk extension.
SOFTWARE QUALITY:
* ROBUSTNESS: Added package system tests for createLink().
Version: 1.29.2 [2014-01-12]
NEW FEATURES:
* Now Arguments$getCharacters() preserves attributes. Also, made argument
'useNames' defaults to TRUE.
* Added [() for GenericSummary.
Version: 1.29.1 [2014-01-10]
NEW FEATURES:
* Added argument 'what' to Sys.readlink2(), where what = "corrected" makes
sure to return the proper target path (not just the one relative to where
the link lives).
Version: 1.29.0 [2014-01-07]
* The following file I/O methods follows symbolic links (also on Windows)
and returns information based on the target file/directory (rather than
the link itself): fileAccess(), file.info2(), isDirectory(), isFile()
and lastModified().
* Added file.info2() for retrieving file information such that symbolic
file links are also acknowledged on Windows.
* Added Sys.readlink2() for reading symbolic file links also on Windows.
* removeDirectory() can now be used to remove symbolic directory links
(also on Windows where neither file.remove() nor unlink() work).
The target directory will never be removed.
* BUG FIX: renameFile() would give an error on directories.
* Added package system tests for copyFile() and renameFile().
* ROBUSTNESS: createLink() will no longer try to create Windows file
links on non-Windows platforms.
* ROBUSTNESS: Updated a shell() calls that assume the Windows command
interpreter to explicitly specify shell = Sys.getenv("COMSPEC").
Version: 1.28.6 [2014-01-06]
* Added argument 'skip' (in addition to existing 'overwrite') to copyFile()
to allow for better control on how to handle existing destination files.
For backward compatibilities, it defaults to FALSE, but may be changed
to skip = !overwrite in a future version. Furthermore, copyFile() now
passes (known) arguments '...' to base::file.copy() making it possible
to copy with or without file permissions etc. Thanks Taku Tokuyasu (UCSF)
for reporting on this.
Version: 1.28.5 [2013-12-15]
* Now argument 'asGString' for Arguments$getCharacters() defaults to
getOption("Arguments$getCharacters/args/asGString", TRUE). This makes
it possible to disable this feature, even when it is not possible to
directly pass that argument. This will also make it possible to
set the default to FALSE in the future (instead of TRUE as today).
* Added argument 'inherits' to evaluate() for GString. Default
is TRUE for backward compatibility.
Version: 1.28.4 [2013-11-20]
* Minor updates to NAMESPACE file.
Version: 1.28.3 [2013-11-15]
* Added method c() for GenericSummary.
Version: 1.28.2 [2013-11-15]
* CLEANUP: Arguments$getNumerics(NA, range = c(0,1)) no longer gives
warnings on "no non-missing arguments to min()" etc.
Version: 1.28.1 [2013-10-30]
* BUG FIX: System$getMappedDrivesOnWindows() failed to return the
proper path for 'net use' mounted drives, iff the path contained
spaces.
Version: 1.28.0 [2013-10-20]
* CLEANUP: Removed a few non-used internal objects.
* Forgot to declare enterf() for Verbose as an S3 method.
Version: 1.27.6 [2013-10-13]
* CLEANUP: Some methods had to attach 'R.utils' in the past in order
to work properly. These are no longer attaching 'R.utils':
copyDirectory(), createLink(), createWindowsShortcut(), downloadFile(),
installPackages(), removeDirectory(), and sourceDirectory().
* Bumped up package dependencies.
Version: 1.27.5 [2013-10-07]
* CLEANUP: Now explicitly importing only what is needed in NAMESPACE.
* CLEANUP: Dropped obsolete autoload():s.
* ROBUSTNESS: The overriding of getOption() to become a generic
function does now call base::getOption() in the default, instead
of copy the latter.
* Bumped up package dependencies.
Version: 1.27.4 [2013-09-28]
* Now argument 'recursive' of listDirectory() can also specify the
maximum recursive depth, e.g listDirectory(..., recursive = 5L).
* Now the 'R.utils' Package object is also available when the
package is only loaded (but not attached).