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The canonical form [1] of an R package Makefile includes the
following:
- The first stanza includes R_PKGNAME, R_PKGVER, PKGREVISION (as
needed), and CATEGORIES.
- HOMEPAGE is not present but defined in math/R/Makefile.extension to
refer to the CRAN web page describing the package. Other relevant
web pages are often linked from there via the URL field.
This updates all current R packages to this form, which will make
regular updates _much_ easier, especially using pkgtools/R2pkg.
[1] http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html
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Update to the canonical form of an R package and fix the LICENSE
field.
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Each R package should include ../../math/R/Makefile.extension, which also
defines MASTER_SITES. Consequently, it is redundant for the individual
packages to do the same. Package-specific definitions also prevent
redefining MASTER_SITES in a single common place.
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Changes:
- add and use native symbols for C-code
- naiveBayes() now supports logical variables
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Upstream changes:
Changes in version 1.6-7
fix some bug in handling weights in svm.default
Changes in version 1.6-6
fix numeric issue in classAgreement()
add functions from recommended packages to NAMESPACE
fix bug in svm.default (incorrect handling of subset= argument)
fix bug in predict.svm (new data with NA in response got removed)
residuals are now correctly computed for regression in case of scaled data
Changes in version 1.6-5
hamming.distance() no longer converts input to binary
tune() now uses mean() to aggregate error measures from cross-fold replications
Changes in version 1.6-4
remove library("SparseM") statements in code, use namespace semantics instead
Fix memory leak and uninitialized read error in write.svm()
add warning in predict.svm() if probabilities should be predicted, but the model was not trained with probability = TRUE
add eps to laplace smoothing in predict.naiveBayes() to account for close-zero probabilities also.
use R's random number generator for cross-validation and probability computation instead of the system one.
Changes in version 1.6-3
remove require() statements and dependency on stats
Changes in version 1.6-2
vignettes moved to vignettes folder.
libsvm upgrade to version 3.17, getting rid of stdout and stderr
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Problems found locating distfiles:
Package dfftpack: missing distfile dfftpack-20001209.tar.gz
Package eispack: missing distfile eispack-20001130.tar.gz
Package fftpack: missing distfile fftpack-20001130.tar.gz
Package linpack: missing distfile linpack-20010510.tar.gz
Package minpack: missing distfile minpack-20001130.tar.gz
Package odepack: missing distfile odepack-20001130.tar.gz
Package py-networkx: missing distfile networkx-1.10.tar.gz
Package py-sympy: missing distfile sympy-0.7.6.1.tar.gz
Package quadpack: missing distfile quadpack-20001130.tar.gz
Otherwise, existing SHA1 digests verified and found to be the same on
the machine holding the existing distfiles (morden). All existing
SHA1 digests retained for now as an audit trail.
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Upstream changes:
Changes in version 1.6-1
write.matrix.csr() now accepts a fac argument similar to read.matrix.csr(), writing factor levels instead of the numeric codes.
naiveBayes() uses a numerically more stable formula for calculating the a-posterior probabilities.
predict.naiveBayes() now accepts data with predictors in an order different from the training data, and also ignores variables not in the model (especially the response variable).
svm() checks whether parameters which are passed to the C-code are set to NULL to avoid segfaults.
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* R CMD INSTALL checks if dependent packages are available early on
* in the installation of source packages, thereby giving clearer
error messages.
* R CMD INSTALL --build now names the file in the format used
for Mac OS X binary files on that platform.
* BIC() in package stats4 now also works with multiple fitted models,
analogously to AIC().
* Use of file extension .C for C++ code in packages is now
deprecated: it has caused problems for some 'make's on
case-insensitive file systems (although it currently works
with the recommended toolkits).
* The C function mkCharLenCE now no longer reads past 'len' bytes
(unlikely to be a problem except in user code).
* On systems without any default LD_LIBRARY_PATH (not even
/usr/local/lib), [DY]LIB_LIBRARY_PATH is now set without a trailing colon.
* More efficient utf8ToInt() on long multi-byte strings with
many multi-byte characters.
* aggregate.ts() gave platform-depedent results due to rounding
error for ndeltat != 1.
* package.skeleton() sometimes failed to fix filenames for .R or
.Rd files to start with an alphanumeric.
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clustering, support vector machines, shortest path computation, bagged
clustering, naive Bayes classifier, ...
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