forked from Bioconductor/BiocCheck
-
Notifications
You must be signed in to change notification settings - Fork 0
/
NEWS
315 lines (253 loc) · 12.9 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
CHANGES IN VERSION 1.36.0
-----------------------
NEW FEATURES
o Include size limit checks for data files in `data`, `inst/extdata`, and
`data-raw` folders (@lshep, #167, #67)
o Source package directories that include an `inst/doc` folder with files
are now flagged with an error. `doc` folders are generated during
`R CMD build`.
o The error for packages already hosted on CRAN has been converted to a
warning (@lshep, #177). Any such incoming packages must be removed from CRAN
before the following Bioconductor release.
BUG FIXES AND MINOR IMPROVEMENTS
o Obtain a more complete list of deprecated packages for
`checkDeprecatedPkgs`
o Fix issue with path seperators on Windows ('\\' vs '/') causing the unit
test for `getBiocCheckDir` to report erroneous mismatches (@grimbough, #175)
o Fix bug where the wrong number of functions with length greater than 50
was reported (@grimbough, #182)
o biocViews term suggestions should be a scalar character (@lcolladotor,
#184)
CHANGES IN VERSION 1.34
-----------------------
NEW FEATURES
o Redundant package dependencies checks between `DESCRIPTION` and
`NAMESPACE` have been removed. These are already present in `R CMD check`
as "checking package dependencies".
o Use `callr` to run `BiocCheck` in a separate process, this avoids
interference with loaded packages (@vjcitn, #158)
BUG FIXES AND MINOR IMPROVEMENTS
o Update `checkVigInstalls` and `checkVigBiocInst` to avoid false positives
(@almeidasilvaf, #170).
o Only count non evaluated chunks when there are any present in the
vignette
o Fix false positive WARNING "Import {pkg} in NAMESPACE as well as
DESCRIPTION." where pkg was not in NAMESPACE but it was used using double
colons pkg::function inside an S4 method. (@zeehio, #166)
o Fix bug where inputs to `getDirFile` were vectors in
`checkForValueSection` (@zeehio, #163)
o Allow lookback for matching T/F and exclude list elements, e.g., `list$F`
(@lshep, #161)
o Fix indentation count by excluding yaml front matter from vignettes
(@harpomaxx, #100)
o Update internal documentation of the `BiocCheck-class`
o Fix bug where line numbers were off due to removal of empty lines at
parsing (@lshep, #159)
o Slightly improve sentence counter for Description field check
(@lshep, #160)
o Update documentation links to point to contributions.bioconductor.org
(@LiNk-NY, #157)
CHANGES IN VERSION 1.32
-----------------------
NEW FEATURES
o Add package metadata to main report for easier diagnostics
o `<pkgname>.BiocCheck` folder, created above the package folder, includes
the full report and NAMESPACE suggestions, if available.
o Add check to find any stray `<pkgname>.BiocCheck` folders
o Update doc links and recommendations for additional information in report
o Update `BiocCheck` report to be more brief by only noting the conditions;
details are included in the full report
BUG FIXES AND MINOR IMPROVEMENTS
o Initialize default verbose value (FALSE) for internal reference object
o Flag only hidden '.RData' files as bad files and allow 'myData.RData'
(@hpages, #155)
o Improve internal handling of condition messages with unified mechanism
o Internal improvements to `BiocCheck` mechanism: export `.BiocCheck` object
which contains all conditions, log list, and method for writing to JSON
o Update to changes in R 4.2 `--no-echo` flag
o Make use of `lib.loc` to helper functions that install and load the
checked package
o (1.31.36) Reduce function length count slightly by removing empty lines.
o (1.31.35) Restricted files in `inst` will be flagged with a `WARNING`
instead of an `ERROR`
o (1.31.32) Account for S3 print methods when checking for `cat` usage
o (1.31.31) Single package imports in the NAMESPACE were breaking the code
to get all package imports.
o (1.31.29) Include other import fields from NAMESPACE file when checking
consistency between imports in DESCRIPTION/NAMESPACE.
o (1.31.27) Update and clean up unit tests.
o (1.31.26) Improve load test for the package being checked.
o (1.31.25) Exclude GitHub URLs that end in HTML from external data check.
o (1.31.23) Internal updates to the `require` and `library` check.
o (1.31.22) Remove old code related to running `BiocCheck` on the command
line and update `BiocCheck` documentation.
o (1.31.21) Remove redundant `=` from message to avoid `=` assignment.
o (1.31.20) Add line feed to "Checking function lengths..." message
o (1.31.18) Packages should not download files when loaded or attached.
o (1.31.17) Using '=' for assignment should be avoided and '<-' should be
used instead for clarity and legibility.
o (1.31.16) Note the use of `cat` and `print` outside of show methods.
o (1.31.15) Check for pinned package versions in the `DESCRIPTION` file
denoted by the use of `==`.
o (1.31.14) Enhancements to internal helper functions and
`BiocCheckGitClone`
o (1.31.13) Revert move to new package checks. Update Bioc-devel mailing
list check to fail early when not in BBS environment.
o (1.31.12) Move Bioc-devel mailing list and support site registration
checks to new package checks.
o (1.31.10) Various internal improvements to `BiocCheck` and the
identification of the package directory and name.
o (1.31.6) Use a more reliable approach to identify package name from the
`DESCRIPTION` file.
o (1.31.5) Fixed bug in the case where the `VignetteBuilder` field in the
a package's `DESCRIPTION` has more than one listed.
o (1.31.3) Add `BioCbooks` repository url to
`checkIsPackageNameAlreadyInUse`, `VIEWS` file is pending.
o (1.31.2) Fix logical length > 1 error in `checkImportSuggestions`
(@vjcitn, #141)
o (1.31.1) Simplify check for function lengths; remove excessive dots.
CHANGES IN VERSION 1.30
-----------------------
NEW FEATURES
o (1.29.10) Check for `Sys.setenv` and `suppressWarnings`/`suppressMessages`
o (1.29.8) Check for `sessionInfo` / `session_info` in vignette code.
o (1.29.5) Check for installation calls in vignette code.
o (1.29.1) Check for `install()` function calls in R code.
BUG FIXES
o (1.29.14) Various internal improvements to the codebase.
o (1.29.12) Checks on class membership code now include `is() ==` grammar.
o (1.29.6) Use appropriate input (`pkgdir`) to internal checking functions.
o (1.29.3) Add unit tests for legacy function searches.
o (1.29.2) rename internal function from checkIsPackageAlreadyInRepo to
checkIsPackageNameAlreadyInUse
CHANGES IN VERSION 1.27
-----------------------
BUG FIX
o (1.27.17) Update support site watched tags. tags are case insensitive
o (1.27.15) Reporting checking of vignette despite package type
(@lshep, #136)
o (1.27.9) Allow portability of child Rmd documents via parseFile
o (1.27.3) Correct check for if package already exists in CRAN/Bioc
o (1.27.3) Correct check for single colon use
o (1.27.2) Correct path to R license database file by calling
R.home('share').
NEW FEATURES
o (1.27.16) Check vignettes for all package types (@lshep, #136)
o (1.27.12) Check for `LazyData: TRUE` in the DESCRIPTION (@lshep, #128)
o (1.27.11) R version dependency check in the 'DESCRIPTION' is now a
'NOTE' (@lshep, #126)
o (1.27.10) Check for 'error' and other keywords in signaler functions,
'message', 'warning', and 'stop' etc. (@hpages, #125)
o (1.27.8) Check for 'tests' entry in '.Rbuildignore'
o (1.27.7) Removed BiocCheck and BiocCheckGitClone installation scripts;
recommended usage is `BiocCheck()`
o (1.27.6) Check that a user has the package name in watched tags of
support site
o (1.27.5) Check for 'paste' / 'paste0' in signaler functions, 'message',
'warning', and 'stop' (@LiNk-NY, #64)
o (1.27.4) Check for downloads from external resources (github, gitlab,
bitbucket, dropbox; @LiNk-NY, #75)
o (1.27.1) Check that licenses do not exclude classes of users,
e.g., non-academic users.
CHANGES IN VERSION 1.25
-----------------------
DEPRECATION ANNOUNCEMENT
o (1.25.11) R CMD BiocCheck and R CMD BiocCheckGitClone are deprecated. The
recommended way to run the functions is within R.
NEW FEATURES
o (1.25.1) Check for warning/notes on too-brief a Description: field
(@federicomarini, #65)
o (1.25.4) Check for single colon typos when using qualified imports
pkg::foo()
o (1.25.8) Validate ORCID iDs (if any) in the DESCRIPTION file
(@LiNk-NY, #97)
o (1.25.10) Add check for properly formatted CITATION file
o (1.25.12) Add NOTE to change dontrun to donttest
BUG FIXES
o (1.25.14) The ORCID iD check now accepts IDs with a X at the end.
o (1.25.9) All packages including infrastructure require a vignette
o Usage of donttest and dontrun in manual pages tagged with the keyword
'internal' will no longer trigger a NOTE (@grimbough, #59)
o (1.25.7) Adding the sessionInfo at the end of the vignette (@llrs)
USER SIGNIFICANT CHANGES
o (1.25.3) Require Aurhors@R format over Author/Maintainer fields in the
DESCRIPTION file. This has been upgraded to an ERROR.
o (1.25.2) Suggest styler over formatR for automatic code re-formatting
(@lcolladotor, #57).
o (1.25.5) Add warning to new package versions with non-zero x version
(@mtmorgan, #101)
CHANGES IN VERSION 1.23
-----------------------
BUG FIX
o (1.23.4) Update locations for NEWS
o (1.23.1) Fix False Positive class == check
CHANGES IN VERSION 1.19
-----------------------
NEW FEATURES
o (1.19.33) Add Authors@R vs Author/Maintainer check
o (1.19.29) Add non evaluated code chunks that have not been executed
because of invalid syntax (```, ```R, ```r). Valid syntax for an evaluated
code chunk takes the form ```{r} or ```{R}.
o (1.19.28) Check that vignette metadata set correctly
o (1.19.27) Check for Author@R or Author/Maintainer but not both
o (1.19.25) Check for use of remotes: in Description
o (1.19.18) Check for use of dontrun/donttest
o (1.19.15) Check vignetteEngine/vignetteBuilder minimially declared in
Suggests
o (1.19.9) Check usage of donttest and dontrun in man page documentation
o (1.19.9) Update deprecated check to check for Bioconductor release and
devel deprecated packages as specified in biocViews
o (1.19.7) More helpful ERROR when using a non valid command line option.
o (1.19.4) All checks module. Ability to turn on/off with flag options. See
'R CMD BiocCheck --help'
o (1.19.1) New Check options to turn off if in CRAN (--no-check-CRAN) and
Bioconductor mailing list and support site (--no-check-bioc-help)
USER SIGNIFICANT CHANGES
o (1.19.8) Updated Documentation in vignette for flag/option controls and
reorganization of code/checks. Grouped similar checks together and changed
order of checks.
o (1.19.3) Remove Native Routine Registrations (use flag in R CMD check
instead _R_CHECK_NATIVE_ROUTINE_REGISTRATION_)
o (1.19.2) Match CRAN standards of package size <= 5MB (updated from 4MB)
BUG FIXES
o (1.19.26) Fix NEWS check to recognize NEWS.md
o (1.19.26) Check all repos for existing package not just software
o (1.19.23) Informative message if no biocViews term found
o (1.19.22) Fix output of system2 usage check
o (1.19.19) Test only closures for T/F
o (1.19.14) Fix ERROR when more than one VignetteEngine found
o (1.19.10) Add suggestion of FormatR package to formatting notes
o (1.19.10) Fix function lengths to be a NOTE and only display if functions
are greater than 50 lines long.
o (1.19.6) Replace use of devtools::create with usethis::create_package as
function was deprecated.
o (1.19.5) Fix length > 1 logical comparison in if statement
CHANGES IN VERSION 1.17
-----------------------
NEW FEATURES
o (1.17.21) Added quit-with-status option to both BiocCheck and
BiocCheckGitClone for compatibility with travis
o (1.17.18) Update devel to use BiocManager instructions instead of
BiocInstaller
o (1.17.17) Add a new function that can be run interactive or command line
BiocCheckGitClone which is only run on a source directory not a
tarball. This will check for bad system files
o (1.17.17) BiocCheck addition: Checks vignette directory for intermediate
and end files that should not be included.
o (1.17.16) Checks for Bioconductor package size requirement if checking
tarball
BUG FIXES
o (1.17.19) Updated internal functions to use BiocManger instead of
BiocInstaller
CHANGES IN VERSION 1.16
-----------------------
BUG FIXES
o handle interactive BiocCheck() arguments correctly
CHANGES IN VERSION 1.14
-----------------------
NEW FEATURES
o NOTE when maintainer subscription to bioc-devel mailing list
cannot be checked (checking requires mailing list admin
password).
BUG FIXES
o Use shell quotes to allow spaces in package paths