Version 1.7.6 (2026-01-22) + 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 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 1.0.1 (2011-11-28) + Add data.frame and matrix manipulation methods + Updated the fme_cor function, although it is not finished.