Changes in version 1.7.8 o Address CRAN feedback for package submission o Quote software names ('Bioinfo-C' and 'BIOS') in DESCRIPTION o Add missing @return tags to cutreeIntoOrderedGroups, invertList, pAbsLog10Score, pQnormScore, and pScore o Replace \dontrun{} with \donttest{} in examples where appropriate o Remove if(interactive()) wrappers from non-interactive examples o Add on.exit() for options restoration in scriptInit() o Change dump.frames() in scriptInit() to write to tempdir() o Replace installed.packages() with requireNamespace() in libordie() o Fix overwriteDir examples to avoid deleting session tempdir() o run pkgdown also in the devel branch Changes in version 1.7.7 (2026-02-03) o Fix mmatch to return indices in consistent order across platforms o Add platform note to mmatch and matchColumnIndex documentation o Fix CRAN pragma issue and Windows test failures Changes in version 1.7.6 o Strengthen CI/CD pipeline with updated GitHub Actions workflows o Fix compilation issues with FORTIFY_SOURCE and Rprintf calls o Fix C warnings and improve compatibility o Add pkgdown documentation site support o Prepare package for CRAN submission Changes in version 1.0-48 o strings in trim.c was freed after they are created by strdup Changes in version 1.0-47 o The package is fully compatible now with bioinfolib (i.e. public version of bios) and tested for the new bioinformatics server Changes in version 1.0-44 o Add \code{assertDesign}, \code{assertContrast}, and \code{assertDesignContrast} o Start using Roxygen2 to make inline documentations (really a cool tool!) Changes in version 1.0-43 o 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. o (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. o Add silencio, a small helper function to keep function running quitely. Changes in version 1.0-42 o Modify summarizeRows and summarizeColumns so that they accept additional parameters and pass them to the function Changes in version 1.0-41 o Add chosenFew to print long vectors Changes in version 1.0-40 o longdf2matrix is updated to be more efficient. Instead of using 'reshape', it builds the matrix directly by populating the elements. Changes in version 1.0-39 o scriptInit set options(warn=-1) in order to supress unwanted warnings o add createDir for scripting Changes in version 1.0-38 o doLog updates Changes in version 1.0-36 o writeLog and doLog use 'fmt' as the first parameter Changes in version 1.0-35 o 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. Changes in version 1.0-34 o assertFile and assertDir returns invisible \code{TRUE} in case the files/directories exist. o basefilename and extname add option 'lower.case' o Add writeLog to write loggings Changes in version 1.0-33 o keepMaxStatRow has been refactored, giving isMaxStatRow (keepMaxStatRowInd) to return logical/integer vector Changes in version 1.0-32 o Add qsystem to run system commands quietly o Add rmat to remove file/directories at a future time point o Add closeFileDevice() which quietly closes current device o 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. Changes in version 1.0-31 o qqmsg only quits R when the session is not interactive. Changes in version 1.0-30 o openFileDevice use cairo as the PNG engine, since X11 engine does not seem to work in a non-interactive session Changes in version 1.0-29 o summarizeRows and summarizeColumns keep column/row names of the input matrix Changes in version 1.0-28 o Add removeInvarCol to remove invariable columns from a data frame or matrix Changes in version 1.0-27 o Move scriptInit from ribiosArg to ribiosUtils Changes in version 1.0-26 o A substantial update of helping pages. Now almost every function exported by the ribiosUtils package has manuals and examples. o Add longdf2matrix to convert long-format data frame into matrix. o add compTwoVecs to compare two vectors using set operations Changes in version 1.0-25 o Add new function: trim, to trim (strip) leading and/or tailing spaces Changes in version 1.0-24 o Add new function: keepMaxStatRow, as a S4-object-independent implementation of the 'keepMaxStatProbe' function in ribiosExpression.It is faster and more generic. o extname adds an option to allow values other than NA returned if not found. Changes in version 1.0-23 o Internal changes: functions dealing with checking existence of files/directories are centralized in file_dir.R Changes in version 1.0-22 o haltifnot: a typo was fixed in the msg o assertFile: error message is now more informative, printing files that do not exist. Changes in version 1.0-21 o Debugging set.R: mset.R does not fail with a vector as input: the vector is simply returned. Changes in version 1.0-20 o Add haltifnot, a function adapted from 'stopifnot', to print informative error messages Changes in version 1.0-19 o Add matchv, imatch, imatchv, ipmatch, ipmatchv for case-insentative matches Changes in version 1.0-18 o Add munion, mintersect and msetdiff for _m_ultiple-set operations. o Add midentical to test whether all objects are identical Changes in version 1.0-16 o Add mmatch function: It performs efficient multiple matching between vectors using BIOS-C codes. Thanks to Roland Schmucki for sharing C codes. o Documentation and test files were added for mmatch o matchColumnIndex (and consequently matchColumn) uses mmatch for multiple matching, improving speed drastically o Add assertFile, assertDir, isDir, checkDir, checkFile, ... functions for scripting o Add various 'small' functions from on-going projects o Implement half of missing documentations Changes in version 1.0-15 o 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. Changes in version 1.0-14 o Add functions for scripting uses: setDebug, unsetDebug, isDebugging and isIntDebugging Changes in version 1.0-13 o srv/Makevars now use bioenv defined variable names, instead of hard-coding dependencies o Minor change in the pwdecode documentation o The version has been installed on biostat server Changes in version 1.0-12 o Add pwdecode function (with C backend) to decode passwords encypted with pwencode command-line tool o (Internal) pwdecode has a parsimonious Makevar file. And it successfully avoids the die mechanism of BIOS system by providing a imposter macro. Changes in version 1.0-11 o Add matrix2longdf function to convert a matrix into long format data.frame o Add extname function to get extension of file names o Add openFileDevice function to open a display device as a file, preparing to print plots to the file. Changes in version 1.0-10 o Both matchColumnIndex and matchColumn function supports both column index and column names, and the matching of row names. o Both matchColumnIndex and matchColumn supports the multi parameter, specifying the behaviour of function in multiple-matching cases. o matchColumnIndex over-writes the column with the master vector: also in the case of multiple mapping. o Documentations have been added for matchColumn and matchColumnIndex. Changes in version 1.0-9 o Add verbose function to allow verbose-level specific printing of verbose information, especially useful in programs with user interfaces. Changes in version 1.0-8 o 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) Changes in version 1.0-7 o Add isError function for try-error catch blocks o qqmsg tests whether message is empty, if no no message will be print, in order to prevent a blank line to be printed Changes in version 1.0-6 o Remove the dependency on the gsl library, which causes problem when the path is not known. Changes in version 1.0-5 o Add summarizeRows and summarizeColumns to summarize rows/columns by factor o Add the documentation for the dfFactor function. Changes in version 1.0.4 o Add qqmsg (function and documentation) to quitely quit a R session. o add libordie function to silently load a library when possible or kill the R session otherwise Changes in version 1.0.3 o Add the methods package into depend list Changes in version 1.0.1 o Add data.frame and matrix manipulation methods o Updated the fme_cor function, although it is not finished.