NEWS

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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

• doLog updates

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.