#303 |
Cannot convert VectorMutable::iterator to VectorBase::const_iterator
|
Peter
|
defect
|
major
|
yat 0.4
|
utility
|
#305 |
matrix_test and score_test fail on linux
|
Peter
|
defect
|
major
|
yat 0.4
|
utility
|
#306 |
Iterators for utility::matrix
|
Peter
|
request
|
major
|
yat 0.4
|
utility
|
#309 |
templatize SubsetGenerator part I
|
Peter
|
request
|
major
|
yat 0.4
|
classifier
|
#310 |
remove DataLookup2D from SubsetGenerator
|
Markus Ringnér
|
request
|
major
|
yat 0.4
|
classifier
|
#311 |
templatize EnsembleBuilder
|
Markus Ringnér
|
request
|
major
|
yat 0.4
|
classifier
|
#312 |
SVM should not inherit from SupervisedClassifer
|
Markus Ringnér
|
request
|
major
|
yat 0.4
|
classifier
|
#313 |
SVM constructor should be void
|
Peter
|
request
|
major
|
yat 0.4
|
classifier
|
#314 |
SVM::predict should not work on DataLookup2D
|
Markus Ringnér
|
defect
|
major
|
yat 0.4
|
classifier
|
#315 |
Create a SmartPtr<T> class
|
Peter
|
request
|
major
|
yat 0.4
|
utility
|
#316 |
Create an Index class
|
Peter
|
request
|
major
|
yat 0.4
|
classifier
|
#317 |
Use classes Index in DataLookup2D
|
Markus Ringnér
|
request
|
major
|
yat 0.4
|
classifier
|
#318 |
SupervisedClassifier::train take data and target
|
Markus Ringnér
|
request
|
major
|
yat 0.4
|
classifier
|
#321 |
Comparison of Iterators
|
Jari Häkkinen
|
enhancement
|
major
|
yat 0.4
|
utility
|
#328 |
Ticket for testing svn post-commit hook
|
Jari Häkkinen
|
enhancement
|
major
|
|
test
|
#333 |
Remove DataLookup2D in SupervisedClassifier interface
|
Markus Ringnér
|
request
|
major
|
yat 0.4
|
classifier
|
#339 |
Vector: indirect self-assignment)
|
Peter
|
defect
|
major
|
yat 0.4
|
utility
|
#340 |
slim down SupervisedClassifer
|
Peter
|
request
|
major
|
yat 0.4
|
classifier
|
#342 |
remove training_data() etc from interface of Lookups
|
Peter
|
request
|
major
|
yat 0.4
|
classifier
|
#343 |
remove DataLookup2D
|
Peter
|
request
|
major
|
yat 0.4
|
classifier
|
#344 |
Commandline::parse should throw cmd_error
|
Peter
|
enhancement
|
major
|
yat 0.4
|
utility
|
#355 |
installation of config.h is flawed
|
Peter
|
defect
|
major
|
yat 0.5
|
build
|
#356 |
Documentation is not generated issuing 'make doc'
|
Peter
|
defect
|
major
|
yat 0.4.1
|
documentation
|
#359 |
Smooth histogram
|
Peter
|
request
|
major
|
yat 0.5
|
statistics
|
#361 |
Averager class does not support removal of data
|
Jari Häkkinen
|
enhancement
|
major
|
yat 0.5
|
statistics
|
#363 |
Weighted Mutable Matrix
|
Peter
|
discussion
|
major
|
yat 0.5
|
utility
|
#365 |
files doc/*.doxygen are not included in distribution
|
Jari Häkkinen
|
defect
|
major
|
yat 0.4.1
|
build
|
#366 |
specialize percentile (and thereby median indirectly) for weighted iterators
|
Peter
|
request
|
major
|
yat 0.5
|
statistics
|
#368 |
create weighted iterator from two unweighted iterators
|
Peter
|
request
|
major
|
yat 0.5
|
utility
|
#369 |
create unweighted iterator from weighted iterator
|
Peter
|
request
|
major
|
yat 0.5
|
utility
|
#377 |
class for nucleotides
|
Peter
|
request
|
major
|
yat 0.7
|
omic
|
#378 |
FileUtil::exists() fails on large files
|
Jari Häkkinen
|
defect
|
major
|
yat 0.4.2
|
utility
|
#381 |
Generalize Kernel_MEV
|
Peter
|
request
|
major
|
yat 0.12
|
utility
|
#389 |
failure in matrix_lookup_test
|
Peter
|
defect
|
major
|
yat 0.5
|
classifier
|
#391 |
return type in iterator_traits is hard-coded to double
|
Jari Häkkinen
|
enhancement
|
major
|
yat 0.5
|
utility
|
#395 |
Document how to implement a weighted iterator
|
Peter
|
enhancement
|
major
|
yat 0.5
|
documentation
|
#396 |
Interfacing MatrixWeighted with Matrix and MatrixLookupWeighted
|
Peter
|
request
|
major
|
yat 0.5
|
utility
|
#402 |
const conversion in StrideIterator
|
Peter
|
enhancement
|
major
|
yat 0.5
|
utility
|
#415 |
Merge 2D Container
|
Peter
|
request
|
major
|
yat 0.6
|
utility
|
#416 |
Move normalization functions/classes to a new directory
|
Peter
|
enhancement
|
major
|
yat 0.5
|
utility
|
#418 |
OptionArg<double> doesnt allow negative numbers
|
Peter
|
defect
|
major
|
yat 0.5
|
utility
|
#423 |
Local: x is not updated in fit function
|
Peter
|
defect
|
major
|
yat 0.4.2
|
regression
|
#424 |
Chapter 1 title in pdf file says 'Main Page'
|
Jari Häkkinen
|
enhancement
|
major
|
yat 0.5
|
documentation
|
#425 |
Implement qQuantile normalizer
|
Jari Häkkinen
|
enhancement
|
major
|
yat 0.5
|
normalizer
|
#426 |
FileUtil does not compile on Tiger
|
Peter
|
defect
|
major
|
yat 0.5
|
build
|
#429 |
Linear::r2(void) not implemented
|
Peter
|
defect
|
major
|
yat 0.5
|
regression
|
#434 |
Vector::Vector(0) crashes
|
Peter
|
defect
|
major
|
yat 0.5
|
utility
|
#436 |
Change license to GPL 3
|
Jari Häkkinen
|
request
|
major
|
yat 0.5
|
documentation
|
#437 |
Rank Normalization
|
Peter
|
request
|
major
|
yat 0.5
|
normalizer
|
#439 |
sort_index for iterators
|
Peter
|
request
|
major
|
yat 0.5
|
utility
|
#444 |
iterators in lookups
|
Peter
|
request
|
major
|
yat 0.5
|
classifier
|
#445 |
All iterators with value type `DataWeight` should be weighted
|
Peter
|
request
|
major
|
yat 0.5
|
utility
|
#449 |
Add tests to check Concepts
|
Peter
|
request
|
major
|
yat 0.6
|
test
|
#450 |
pearson_p_value returns NaN when correlation is unity
|
Peter
|
defect
|
major
|
yat 0.5
|
statistics
|
#451 |
test yat.m4
|
Peter
|
request
|
major
|
yat 0.5
|
test
|
#457 |
kolmogov_smirnov_test fails on Mac OS 10.4
|
Peter
|
defect
|
major
|
yat 0.5
|
test
|
#458 |
documentation_test.sh check fails
|
Jari Häkkinen
|
defect
|
major
|
yat 0.5
|
test
|
#459 |
DiscreteGeneral has pointer but no declared copy constructor (or assignment operator)
|
Jari Häkkinen
|
defect
|
major
|
yat 0.5
|
random
|
#460 |
Fisher::oddsratio returns zero
|
Peter
|
defect
|
major
|
yat 0.4.3
|
statistics
|
#461 |
Fisher::p_value is incorrect
|
Peter
|
defect
|
major
|
yat 0.4.3
|
statistics
|
#463 |
Improve the documentation of Matrix(istream&,char)
|
Jari Häkkinen
|
defect
|
major
|
yat 0.5
|
documentation
|
#464 |
WeNNI does not handle NaNs well
|
Jari Häkkinen
|
defect
|
major
|
yat 0.5
|
utility
|
#466 |
Add interface to GSL interpolation functionality
|
Jari Häkkinen
|
enhancement
|
major
|
yat 0.5
|
regression
|
#472 |
extend make release target
|
Peter
|
request
|
major
|
yat 0.5
|
build
|
#474 |
create Vector from temporary VectorView fails
|
Peter
|
request
|
major
|
yat 0.15
|
utility
|
#476 |
NNI algorithms return wrong number of rows not imputed
|
Jari Häkkinen
|
discussion
|
major
|
yat 0.5
|
test
|
#488 |
Container2DIterator::dereference returns reference to temporary
|
Peter
|
defect
|
major
|
yat 0.5
|
utility
|
#491 |
allow --without in yat.m4
|
Peter
|
request
|
major
|
yat 0.6
|
build
|
#492 |
documentation_test.sh check fails: doxygen \tparam command unknown?
|
Peter
|
defect
|
major
|
yat 0.5
|
documentation
|
#493 |
class for Spearman correlation
|
Peter
|
request
|
major
|
yat 0.9
|
statistics
|
#494 |
Class for Kendall's tau
|
Peter
|
request
|
major
|
yat 0.9
|
statistics
|
#496 |
YAT_LTLINK_IFELSE
|
Peter
|
request
|
major
|
yat 0.7
|
m4
|
#498 |
mixing weighted and unweighted iterators in normalizers
|
Peter
|
discussion
|
major
|
yat 0.6
|
normalizer
|
#500 |
yat_m4_test.sh fails under VPATH build
|
Peter
|
defect
|
major
|
yat 0.6
|
test
|
#501 |
doxygen should only read header files that will be installed
|
Peter
|
enhancement
|
major
|
yat 0.6
|
build
|
#503 |
IGP does not compile (was: add test for IGP)
|
Peter
|
defect
|
major
|
yat 0.5.2
|
classifier
|
#507 |
getline input iterator
|
Peter
|
request
|
major
|
yat 0.6
|
utility
|
#510 |
funtion creating vector<vector<T>> from istream
|
Peter
|
request
|
major
|
yat 0.6
|
utility
|
#511 |
linking statically against atlas fails on Fedora
|
Jari Häkkinen
|
defect
|
major
|
yat 0.6
|
build
|
#512 |
use doxygen tag \relates
|
Peter
|
request
|
major
|
yat 0.6
|
documentation
|
#513 |
Documentation of qQuantileNormalization does not clearly explain what the target is
|
Jari Häkkinen
|
enhancement
|
major
|
yat 0.5.3
|
documentation
|
#517 |
Improve docs on Option classes
|
Peter
|
request
|
major
|
yat 0.6
|
documentation
|
#518 |
choosing cblas - when and how?
|
Jari Häkkinen
|
discussion
|
major
|
yat 0.6
|
build
|
#520 |
A class to redirect streams easily.
|
Peter
|
request
|
major
|
yat 0.6
|
utility
|
#525 |
update macros in yat.m4 to reflect that libyat no longer has a dependency to a cblas lib
|
Peter
|
request
|
major
|
yat 0.6
|
m4
|
#526 |
configure says I have gsl installed (but too old) although I just removed it
|
Peter
|
defect
|
major
|
yat 0.6
|
build
|
#527 |
Cannot run configure on 64-bit CentOS
|
Jari Häkkinen
|
defect
|
major
|
yat 0.5.3
|
build
|
#528 |
make check fails in 0.5-stable branch
|
Jari Häkkinen
|
defect
|
major
|
yat 0.5.3
|
test
|
#529 |
Document important configure options
|
Peter
|
enhancement
|
major
|
yat 0.6
|
build
|
#531 |
creation of doxygen.mk files is not portable
|
Peter
|
defect
|
major
|
yat 0.6
|
build
|
#532 |
m4 files are missing in list of requirements in yat_add*test.sh
|
Peter
|
defect
|
major
|
yat 0.6
|
test
|
#533 |
CommandLine parse(argc, argv) gives bus error if I I have no write privileges to the result directory
|
Peter
|
defect
|
major
|
yat 0.5.3
|
utility
|
#536 |
sorting range with NaNs does not behave as desired
|
Jari Häkkinen
|
defect
|
major
|
yat 0.6
|
utility
|
#537 |
repeated make clean fails
|
Peter
|
defect
|
major
|
yat 0.6
|
build
|
#538 |
commandline_test fails when running as root
|
Peter
|
defect
|
major
|
yat 0.5.4
|
test
|
#542 |
behavior and documentation of SVM::predict are not consistent
|
Peter
|
defect
|
major
|
yat 0.5.5
|
classifier
|
#543 |
deprecate MatrixLookup(Matrix, Index, bool) and friends
|
Peter
|
discussion
|
major
|
yat 0.7
|
classifier
|
#548 |
make doc gets stuck in latex prompt
|
Jari Häkkinen
|
defect
|
major
|
yat 0.5.4
|
documentation
|
#549 |
./yat_cxx_add_flag_test.sh fails
|
Peter
|
defect
|
major
|
yat 0.6
|
test
|
#550 |
do not hard code return type and argument types in compose_f_gx_hy
|
Peter
|
enhancement
|
major
|
yat 0.6
|
utility
|