This repository has been archived by the owner on Dec 6, 2022. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathNEWS
152 lines (116 loc) · 5.68 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
Changes in version 1.6.1 (2022-11-22)
+ Upgrade deprecated methods.
+ Remove R_front script.
Changes in version 1.3.3 (2022-04-02)
+ Explain how to use custom CSV file in vignette.
Changes in version 1.3.2 (2022-03-11)
+ Correct ext pkg upgrade: do not generate C++ example files again.
+ Change default vignette name to package name.
+ When upgrading a extension package, do not generate C++ files again.
+ Accept an unknown total in Progress class.
+ isSearchableByField() accepts field.type param now.
Changes in version 1.3.1 (2021-12-10)
+ Remove custom cache folder setting in vignette.
Changes in version 1.1.17 (2021-10-22)
+ Correct running of long tests.
Changes in version 1.1.16 (2021-10-19)
+ Update documentation.
+ Add ORCID for Alexis.
Changes in version 1.1.15 (2021-10-18)
+ Correct getUrlContent() to handle binary files.
Changes in version 1.1.14 (2021-10-17)
+ Factorize RCurl calls into global functions.
+ Disable warnings in calls to readLines() when using base::url().
+ Catch errors when trying to set locale.
+ Correct some tests.
Changes in version 1.1.13 (2021-10-12)
+ Make custom persistent the cache the default, following slowness with BiocFileCache in biodbHmdb.
+ Remove useless bib refs in vignettes/references.bib.
+ Add session info in vignettes.
+ Add ORCID, URL and BugReports.
+ Add an install section in main vignette.
Changes in version 1.1.12 (2021-10-09)
+ Switch back to custom implementation of persistent cache, following errors with BiocFileCache on Windows and also slowness with HMDB.
Changes in version 1.1.11 (2021-10-07)
+ Decompose test test.collapseRows() because of error on Bioconductor not reproduced on local computer.
Changes in version 1.1.10 (2021-09-30)
+ Disable UniProt request test: it fails (result is NA) for reason unknown only on Bioconductor Linux server during "R CMD check". Works fine on local computer.
Changes in version 1.1.9 (2021-09-28)
+ Correct handling of wrong URL with base::url().
Changes in version 1.1.8 (2021-09-28)
+ Correct bug of UniProt request on Windows.
Changes in version 1.1.7 (2021-09-23)
+ Ignore build folder when building package.
+ Update documentation.
+ Correct setting of R_ENVIRON_USER when building.
Changes in version 1.1.6 (2021-09-14)
+ Update documentation.
Changes in version 1.1.5 (2021-09-13)
+ Correct bug in return type of BiodbRequestScheduler::sendRequest().
+ Correct encoding of test reference filenames.
Changes in version 1.1.4 (2021-09-12)
+ Allow to set the test reference folder directly into runGenericTests(). This
is now necessary for running generic tests in extension packages.
Changes in version 1.1.3 (2021-09-12)
+ Set package name when calling runGenericTests() in order to find test ref
files the correct way, by calling system.file().
Changes in version 1.1.2 (2021-09-09)
+ Use BiocFileCache for the persistent cache system.
+ Switch to R6.
+ Define do...() private methods to be redefined in subclasses, instead of
redefining public methods defined inside super class.
+ Use now local entry files for testing parsing of entry fields.
Changes in version 1.1.1 (2021-06-10)
+ Allow skipping of some fields when testing searchForEntries().
+ Move test reference entries folder from tests/testthat/res to inst/testref.
+ Move long tests folder from tests/long to longtests and enable Bioconductor
long tests.
Changes in version 1.0.4 (2021-06-09)
+ Bug fix: correct call to logger in BiodbPersitentCache class.
Changes in version 1.0.3 (2021-05-26)
+ Bug fix: correct generic test of searchForEntries(), allowing testing with NA
value.
Changes in version 1.0.2 (2021-05-23)
+ Bug fix: correct return type of searchForEntries(), which now returns always
a character vector and never NULL.
Changes in version 1.0.1 (2021-05-20)
+ Bug fix: correct some calls to logging functions that raised a warning.
Changes in version 0.99.11 (2021-05-17)
+ Change example inside BiodbConfig to avoid misinterpretation of
`set('cache.directory', '~/my.biodb.cache')`, leading to believe that some
files are written inside USER HOME folder when running the example.
Changes in version 0.99.10 (2021-05-07)
+ Correct documentation of C++ function.
Changes in version 0.99.9 (2021-05-07)
+ Solving some NOTES from BiocCheck.
+ Correct example in Progress class.
Changes in version 0.99.8 (2021-05-06)
+ Correct template travis.yml for extensions: missing deps install, run all
checks.
+ Improve template Makefile for extensions.
+ Add missing test-cpp.R template file for running C++ tests from testthat.
+ Limit by default the entries to test to one entry inside generic tests.
+ Improve vignettes.
+ Rename default vignette into "biodb.Rmd".
Changes in version 0.99.7 (2021-04-27)
+ Renamed Biodb class into BiodbMain in order to avoid "Rd warning: Previous
alias or file overwritten by alias: biodb" on Windows platform.
+ Implement newInst() global function for creating new BiodbMain instance.
Changes in version 0.99.6 (2021-04-27)
+ Rebuilding doc.
Changes in version 0.99.5 (2021-04-27)
+ Add missing parameters documentation for runGenericTests().
Changes in version 0.99.4 (2021-04-27)
+ Move long tests to separate directory "long".
Changes in version 0.99.3 (2021-04-27)
+ Added "biodb" as watched tag on my profile on support site
https://support.bioconductor.org/.
Changes in version 0.99.2 (2021-04-27)
+ Switch to MassBank extract for testing MassCsvFile and MassSqlite connectors.
Changes in version 0.99.1 (2021-04-26)
+ Remove Git files refused by BiocCheckGitClone.
+ Use CHECK_RENVIRON in local tests.
+ Correct condition in BiodbEntryFields::getRealName() that did not pass check.
+ Add all doc files man/*.Rd for BiocCheck run on http://bioconductor.org.
Changes in version 0.99.0 (2021-04-22)
+ Submitted to Bioconductor