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ChangeLog
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2024-11-08 Jan Lisec <[email protected]>
* Rdisop-1.67.4
* fix for issue #33; use R based random number calls in a CRAN approved way.
2024-11-08 Jan Lisec <[email protected]>
* Rdisop-1.67.3
* fix for issue #20; a wrongly specified `maxisotopes` parameter will not
crash R but return an error instead
* fix for issue #12 and issue #5; `decomposeIsotopes` help section now better
explains how to define elemental limits specified via `minElements` and
`maxElements`
* `maxElements`does respect now an upper limit of zero (basically another way
to exclude elements, which could be achieved before only by not defining the
element in the first place, which caused trouble for CHNOPS elements which
are always expected by disop.cpp)
* fix for issue #1; `getMolecule` and `addMolecules` do check the elements of
the provided formulas now and use only the minimal required elemental set
to process the result. This prevents crashes that happend when the full PSE
was initialized due to problems with atoms having exatly 7 isotopes in their
definition.
2024-11-05 Jan Lisec <[email protected]>
* Rdisop-1.67.2
* fix for issue #21; `decomposeIsotopes` modified the object provided as
parameter `intensities`
2024-10-18 Jan Lisec <[email protected]>
* Rdisop-1.67.1
* !changed `getIsotope` function to return a list of matrices to be
consistent with the other getter functions
* new exported function `getMonoisotopic()` which will return the mono-isotopic mass
for a molecule object (also when a list of molecules as for decomposeMass)
or alternatively for a vector of chemical formulas
* modified documentation to clarify the difference of exactmass and mono-
isotopic mass
* `testthat` tests for `getMonoisotopic` were set up
* `getMolecule` is now testing the provided formula parameter to avoid crashes
on the C++ level (addressing issue #3)
* new internal function to count chemical elements (imported/copied from the
CorMID package) to be utilized in `getMonoisotopic` and `getMolecule`
* two data sets included in package and appropriately documented
* `isotopes` (a data.frame version of the PSE info)
* `mono_masses` (a named vector containing only the most abundant isotope per
element)
2024-10-10 Jan Lisec <[email protected]>
* Rdisop-1.65.3
* getMolecule now respects the charge parameter z
* exact masses will be corrected by z times the electron mass
* isotope masses will be additionally devided in case of abs(z)>=2
* a `testthat` function for getMolecule was set up
* the documentation for getMolecule was updated
* previous users will be informed by a message when calling getMolecule with z!=0
2024-10-10 Jan Lisec <[email protected]>
* Rdisop-1.65.2
* all R functions grouped to separate individual files
* all R functions documented using roxygen2
* `testthat` based testing environment set up
* Rdisop.dll bound to R using R_useDynamicSymbols()
* Vignette converted to Rmd format
* GitHub actions included
2024-09-16 Miao Yu
* fix C++-17 issue on recent compilers reported by Prof. Ripley
2024-05-16 Miao Yu
* fix cpp Rferror issues with help of @vjcitn
2023-02-12 Steffen Neumann <sneumann@msbi-corei>
* search&replace deprecated auto_ptr with unique_ptr
* use labda functions instead of e.g. bind2nd()
2019-05-02 Steffen Neumann <sneumann@msbi-corei>
* Rdisop-1.45.1: Merge fix by Max Helf for improved
decomposeMass: element filter handling.
2019-04-01 Steffen Neumann <sneumann@msbi-corei>
* Rdisop-1.43.2: David Rasp helped to remove dependency
to RcppClassic, which might not be supported at some time
in the future
2015-12-08 Steffen Neumann <[email protected]>
* Added unit test for charge=0 and charge=1
2012-10-26 Steffen Neumann <[email protected]>
* /inst/doc -> /vignettes: to please lates R devel
* src/ims/distributionprobabilityscorer.cpp: remove stdout messages
2012-10-26 Steffen Neumann <[email protected]>
* src/disop.cpp (decomposeIsotopes): Add support for element count filtering
2012-04-21 Steffen Neumann <[email protected]>
* R/elements.R (initializeCharges): Fixed electron mass
2012-03-28 Steffen Neumann <[email protected]>
* Added citations in package and documentation
2012-03-26 Steffen Neumann <[email protected]>
* src/disop.cpp: fixed missing UNPROTECT(), avoids warning
and possibly memory corruprtion and crashes
2012-03-11 Steffen Neumann <[email protected]>
* Reverted Windows build hack
2012-03-10 Steffen Neumann <[email protected]>
* Windows build hack
2012-03-06 Steffen Neumann <[email protected]>
* Windows build fixes, removed old configure.in
2012-02-23 Steffen Neumann <[email protected]>
* Moved from the ancient embedded Rcpp to RcppClassic,
thanks to the work of Dirk Eddelbuettel who did the porting
2010-11-04 Steffen Neumann <[email protected]>
* Corrected bug that leads to wrong monoisotopic masses for molecules
containing elements where the most abundant isotope is not the first one,
discovered by Ralf Tautenhahn
2010-10-22 Steffen Neumann <[email protected]>
* R/elements.R: Added remaining elements to PSE,
contributed by Canteri Roberto (http://m2b2.fbk.eu/en/people)
2010-05-18 Steffen Neumann <[email protected]>
* added Runit test infrastructure
2010-04-02 Steffen Neumann <[email protected]>
* added Selenium to list of elements
* added Cobalt to list of elements
* fixed Selenium abundances and masses
2010-02-08 Steffen Neumann <[email protected]>
* added parameter maxisotopes to getMolecule() and decompose*()
2008-09-02 ckuhl <[email protected]>
* R/elements.R: added Deuterium
2008-08-11 sneumann <[email protected]>
* R/elements.R (initializeCharges): added initializeCharges, which
can be useful for getMolecule("H3O+", elements=c(initializeCHNOPS(),initializeCharges()))
* R/Rdisop.R: fixed important bug which always initialised the
full PSE when supplying a special elements list
2008-04-23 sneumann <[email protected]>
* R/elements.R: fixed some masses/abundances,
added more elements
2008-02-15 sneumann <[email protected]>
* R/elements.R (initializePSE): Fixed Mass of Na isotope
2007-12-04 sneumann <[email protected]>
* configure.win, src/Makevars.win, src/win/*: Fix Windows build
2007-12-04 sneumann <[email protected]>
* R/Rdisop.R, man/decomposeMass.Rd: added absolute mass deviation
2007-10-29 begert <[email protected]>
* R/elements.R: Fixed O mass
2007-10-19 sneumann <[email protected]>
* NAMESPACE: Re-enabled useDynLib(libims) to fix Linux Build
2007-10-15 sneumann <[email protected]>
* configure.win, src/Makevars.win: Fix Windows build
2007-10-14 Steffen Neumann <[email protected]>
* man: fixed some manpages
2007-07-26 sneumann <[email protected]>
* removed several get*Masses in favour of getMass
* polished vignette
2007-07-11 sneumann <[email protected]>
* R/elements.R, R/Rdisop.R: Formatting changes
* configure.in: disabled autogen for imslib
2007-07-09 sneumann <[email protected]>
* DESCRIPTION (Version): bumped Version following BioC scheme
2007-07-03 sneumann <[email protected]>
* src/disop.cpp: Clear error Message before running
2007-06-14 sneumann <[email protected]>
* R/Rdisop.R: removed CHNOPS warning message
* Windows: first Windows build
2007-06-07 sneumann <[email protected]>
* R/Rdisop.R (decomposeMass): fixed call
2007-06-05 sneumann <[email protected]>
* src/disop.cpp: Fixed stack imbalance for empty decompositions
* src/disop.cpp: improved Error Handling
2007-05-25 sneumann <[email protected]>
* R/elements.R: Added na, k, cl, br, f, i, fe, mg, ca
* R/Rdisop.R: moved isotope table to own file
2007-05-15 Steffen Neumann <[email protected]>
* Added addMolecule and subMolecule
to do arithmetics with adducts / fragments
2007-05-04 Steffen Neumann <[email protected]>
* configure.in: Re-Added local copy of IMS as fallback
2007-04-30 Steffen Neumann <[email protected]>
* R/zzz.R: removed unnecesary library.dynam()
which also caused problems on systems without libR.so
* src/ims/*: moved imslib sources into src/ subfolder
instead of using unchanged libims.a
2007-03-23 Steffen Neumann <[email protected]>
* src/disop.cpp: Removed decomposeMass(), this case is handled by
the R code.