NEWS
ribiosUtils 1.7.8
- Address CRAN feedback for package submission
- Quote software names ('Bioinfo-C' and 'BIOS') in DESCRIPTION
- Add missing @return tags to cutreeIntoOrderedGroups, invertList,
pAbsLog10Score, pQnormScore, and pScore
- Replace \dontrun{} with \donttest{} in examples where appropriate
- Remove if(interactive()) wrappers from non-interactive examples
- Add on.exit() for options restoration in scriptInit()
- Change dump.frames() in scriptInit() to write to tempdir()
- Replace installed.packages() with requireNamespace() in libordie()
- Fix overwriteDir examples to avoid deleting session tempdir()
- run pkgdown also in the devel branch
ribiosUtils 1.7.7 (2026-02-03)
- Fix mmatch to return indices in consistent order across platforms
- Add platform note to mmatch and matchColumnIndex documentation
- Fix CRAN pragma issue and Windows test failures
ribiosUtils 1.7.6
- Strengthen CI/CD pipeline with updated GitHub Actions workflows
- Fix compilation issues with FORTIFY_SOURCE and Rprintf calls
- Fix C warnings and improve compatibility
- Add pkgdown documentation site support
- Prepare package for CRAN submission
ribiosUtils 1.0-48
- strings in trim.c was freed after they are created by strdup
ribiosUtils 1.0-47
- The package is fully compatible now with bioinfolib (i.e. public version of bios) and tested for the new bioinformatics server
ribiosUtils 1.0-44
- Add \code{assertDesign}, \code{assertContrast}, and \code{assertDesignContrast}
- Start using Roxygen2 to make inline documentations (really a cool tool!)
ribiosUtils 1.0-43
- 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.
ribiosUtils 1.0-42
- Modify summarizeRows and summarizeColumns so that they accept additional parameters and pass them to the function
ribiosUtils 1.0-41
- Add chosenFew to print long vectors
ribiosUtils 1.0-40
- longdf2matrix is updated to be more efficient. Instead of using 'reshape', it builds the matrix directly by populating the elements.
ribiosUtils 1.0-39
- scriptInit set options(warn=-1) in order to supress unwanted warnings
- add createDir for scripting
ribiosUtils 1.0-38
ribiosUtils 1.0-36
- writeLog and doLog use 'fmt' as the first parameter
ribiosUtils 1.0-35
- 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.
ribiosUtils 1.0-34
- 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
ribiosUtils 1.0-33
- keepMaxStatRow has been refactored, giving isMaxStatRow (keepMaxStatRowInd) to return logical/integer vector
ribiosUtils 1.0-32
- 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.
ribiosUtils 1.0-31
- qqmsg only quits R when the session is not interactive.
ribiosUtils 1.0-30
- openFileDevice use cairo as the PNG engine, since X11 engine does not seem to work in a non-interactive session
ribiosUtils 1.0-29
- summarizeRows and summarizeColumns keep column/row names of the input matrix
ribiosUtils 1.0-28
- Add removeInvarCol to remove invariable columns from a data frame or matrix
ribiosUtils 1.0-27
- Move scriptInit from ribiosArg to ribiosUtils
ribiosUtils 1.0-26
- 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
ribiosUtils 1.0-25
- Add new function: trim, to trim (strip) leading and/or tailing spaces
ribiosUtils 1.0-24
- 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.
ribiosUtils 1.0-23
- Internal changes: functions dealing with checking existence of files/directories are centralized in file_dir.R
ribiosUtils 1.0-22
- haltifnot: a typo was fixed in the msg
- assertFile: error message is now more informative, printing files that do not exist.
ribiosUtils 1.0-21
- Debugging set.R: mset.R does not fail with a vector as input: the vector is simply returned.
ribiosUtils 1.0-20
- Add haltifnot, a function adapted from 'stopifnot', to print informative error messages
ribiosUtils 1.0-19
- Add matchv, imatch, imatchv, ipmatch, ipmatchv for case-insentative matches
ribiosUtils 1.0-18
- Add munion, mintersect and msetdiff for _m_ultiple-set operations.
- Add midentical to test whether all objects are identical
ribiosUtils 1.0-16
- 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
ribiosUtils 1.0-15
- 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.
ribiosUtils 1.0-14
- Add functions for scripting uses: setDebug, unsetDebug, isDebugging and isIntDebugging
ribiosUtils 1.0-13
- 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
ribiosUtils 1.0-12
- 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.
ribiosUtils 1.0-11
- 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.
ribiosUtils 1.0-10
- 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.
ribiosUtils 1.0-9
- Add verbose function to allow verbose-level specific printing of verbose information, especially useful in programs with user interfaces.
ribiosUtils 1.0-8
- 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)
ribiosUtils 1.0-7
- 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
ribiosUtils 1.0-6
- Remove the dependency on the gsl library, which causes problem when the path is not known.
ribiosUtils 1.0-5
- Add summarizeRows and summarizeColumns to summarize rows/columns by factor
- Add the documentation for the dfFactor function.
ribiosUtils 1.0.4
- 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
ribiosUtils 1.0.3
- Add the methods package into depend list
ribiosUtils 1.0.1
- Add data.frame and matrix manipulation methods
- Updated the fme_cor function, although it is not finished.