-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathNEWS
162 lines (118 loc) · 7.92 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
Version 1.0-48 (2015-06-02)
+ strings in trim.c was freed after they are created by strdup
Version 1.0-47 (2015-05-05)
+ The package is fully compatible now with bioinfolib (i.e. public version of bios) and tested for the new bioinformatics server
Version 1.0-44 (2014-10-30)
+ Add \code{assertDesign}, \code{assertContrast}, and \code{assertDesignContrast}
+ Start using Roxygen2 to make inline documentations (really a cool tool!)
Version 1.0-43 (2014-08-15)
+ registerLog adds an extra option, append=FALSE, to provide alternative behavior to the logging machinary. Note that the default behaviour has changed from this version: previously files are only appended and never overwritten; from now on an existing file will be overwritten unless the append option is manually set to TRUE.
+ (Internal) add appendLogger function, which checks redundancy of loggers by the connection description string, in order to avoid appending loggers that have been in the list again.
+ Add silencio, a small helper function to keep function running quitely.
Version 1.0-42 (2014-08-08)
+ Modify summarizeRows and summarizeColumns so that they accept additional parameters and pass them to the function
Version 1.0-41 (2014-07-30)
+ Add chosenFew to print long vectors
Version 1.0-40 (2014-06-30)
+ longdf2matrix is updated to be more efficient. Instead of using 'reshape', it builds the matrix directly by populating the elements.
Version 1.0-39 (2014-04-14)
+ scriptInit set options(warn=-1) in order to supress unwanted warnings
+ add createDir for scripting
Version 1.0-38 (2014-01-28)
+ doLog updates
Version 1.0-36 (2014-01-24)
+ writeLog and doLog use 'fmt' as the first parameter
Version 1.0-35 (2014-01-20)
+ Add a generic logging mechanism. User (especially script programmer) can use registerLog/doLog to write log messages into arbitrary number of loggers, which can be either files or connections.
Version 1.0-34 (2014-01-10)
+ assertFile and assertDir returns invisible \code{TRUE} in case the files/directories exist.
+ basefilename and extname add option 'lower.case'
+ Add writeLog to write loggings
Version 1.0-33 (2013-08-14)
+ keepMaxStatRow has been refactored, giving isMaxStatRow (keepMaxStatRowInd) to return logical/integer vector
Version 1.0-32 (2013-07-24)
+ Add qsystem to run system commands quietly
+ Add rmat to remove file/directories at a future time point
+ Add closeFileDevice() which quietly closes current device
+ openFileDevice() now sets useDingbat=FALSE by default for PDF outputs in order to achieve better compatibility with SVG files, and sets dpi as a parameter.
Version 1.0-31 (2013-07-19)
+ qqmsg only quits R when the session is not interactive.
Version 1.0-30 (2013-07-17)
+ openFileDevice use cairo as the PNG engine, since X11 engine does not seem to work in a non-interactive session
Version 1.0-29 (2013-06-27)
+ summarizeRows and summarizeColumns keep column/row names of the input matrix
Version 1.0-28 (2013-05-16)
+ Add removeInvarCol to remove invariable columns from a data frame or matrix
Version 1.0-27 (2013-05-15)
+ Move scriptInit from ribiosArg to ribiosUtils
Version 1.0-26 (2013-02-19)
+ A substantial update of helping pages. Now almost every function exported by the ribiosUtils package has manuals and examples.
+ Add longdf2matrix to convert long-format data frame into matrix.
+ add compTwoVecs to compare two vectors using set operations
Version 1.0-25 (2012-12-04)
+ Add new function: trim, to trim (strip) leading and/or tailing spaces
Version 1.0-24 (2012-11-19)
+ Add new function: keepMaxStatRow, as a S4-object-independent implementation of the 'keepMaxStatProbe' function in ribiosExpression.It is faster and more generic.
+ extname adds an option to allow values other than NA returned if not found.
Version 1.0-23 (2012-11-02)
+ Internal changes: functions dealing with checking existence of files/directories are centralized in file_dir.R
Version 1.0-22 (2012-10-24)
+ haltifnot: a typo was fixed in the msg
+ assertFile: error message is now more informative, printing files that do not exist.
Version 1.0-21 (2012-10-22)
+ Debugging set.R: mset.R does not fail with a vector as input: the vector is simply returned.
Version 1.0-20 (2012-10-17)
+ Add haltifnot, a function adapted from 'stopifnot', to print informative error messages
Version 1.0-19 (2012-10-03)
+ Add matchv, imatch, imatchv, ipmatch, ipmatchv for case-insentative matches
Version 1.0-18 (2012-10-02)
+ Add munion, mintersect and msetdiff for _m_ultiple-set operations.
+ Add midentical to test whether all objects are identical
Version 1.0-16 (2012-06-22)
+ Add mmatch function: It performs efficient multiple matching between vectors using BIOS-C codes. Thanks to Roland Schmucki for sharing C codes.
+ Documentation and test files were added for mmatch
+ matchColumnIndex (and consequently matchColumn) uses mmatch for multiple matching, improving speed drastically
+ Add assertFile, assertDir, isDir, checkDir, checkFile, ... functions for scripting
+ Add various 'small' functions from on-going projects
+ Implement half of missing documentations
Version 1.0-15 (2012-06-20)
+ matchColumnIndex is not a little more efficient in doing the multiple matching. However it requires substantion re-coding in C to make it as efficient as normal match. The work is ongoing.
Version 1.0-14 (2012-06-06)
+ Add functions for scripting uses: setDebug, unsetDebug, isDebugging and isIntDebugging
Version 1.0-13 (2012-05-07)
+ srv/Makevars now use bioenv defined variable names, instead of hard-coding dependencies
+ Minor change in the pwdecode documentation
+ The version has been installed on biostat server
Version 1.0-12 (2012-03-22)
+ Add pwdecode function (with C backend) to decode passwords encypted with pwencode command-line tool
+ (Internal) pwdecode has a parsimonious Makevar file. And it successfully avoids the die mechanism of BIOS system by providing a imposter macro.
Version 1.0-11 (2012-03-09)
+ Add matrix2longdf function to convert a matrix into long format data.frame
+ Add extname function to get extension of file names
+ Add openFileDevice function to open a display device as a file, preparing to print plots to the file.
Version 1.0-10 (2012-02-10)
+ Both matchColumnIndex and matchColumn function supports both column index and column names, and the matching of row names.
+ Both matchColumnIndex and matchColumn supports the multi parameter, specifying the behaviour of function in multiple-matching cases.
+ matchColumnIndex over-writes the column with the master vector: also in the case of multiple mapping.
+ Documentations have been added for matchColumn and matchColumnIndex.
Version 1.0-9 (2012-02-06)
+ Add verbose function to allow verbose-level specific printing of verbose information, especially useful in programs with user interfaces.
Version 1.0-8 (2012-01-18)
+ The library function is checked for the support of "quietly" option in libordie by checking the base package version (>=2.13.0 supports quietly=TRUE)
Version 1.0-7 (2011-12-21)
+ Add isError function for try-error catch blocks
+ qqmsg tests whether message is empty, if no no message will be print, in order to prevent a blank line to be printed
Version 1.0-6 (2011-12-19)
+ Remove the dependency on the gsl library, which causes problem when the path is not known.
Version 1.0-5 (2011-12-19)
+ Add summarizeRows and summarizeColumns to summarize rows/columns by factor
+ Add the documentation for the dfFactor function.
Version 1.0.4 (2011-12-16)
+ Add qqmsg (function and documentation) to quitely quit a R session.
+ add libordie function to silently load a library when possible or kill the R session otherwise
Version 1.0.3 (2011-12-15)
+ Add the methods package into depend list
Version 1.0.2 (skipped since no stable release was made)
Version 1.0.1 (2011-11-28)
+ Add data.frame and matrix manipulation methods
+ Updated the fme_cor function, although it is not finished.