CRAN packages maintained by you
Kurt Hornik
Kurt.Hornik at wu.ac.at
Fri Feb 5 12:12:47 CET 2010
Dear maintainers,
This concerns the packages
BLCOP NADA Ryacas SNPMaP TIMP amba backtest crosshybDetector fBasics
fUtilities filehashSQLite grnnR mmlcr nws portfolio portfolioSim
qualV race tradeCosts
maintained by one of you, which give warnings about code/documentation
mismatches, see below.
Can we pls have updates fixing these within the next 2 weeks?
Note that other R CMD check problems may need to be addressed as well.
Best
-k
**********************************************************************
Package: BLCOP Version: 0.2.2 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'BLResult-class':
Slots for class 'BLResult'
Code: kappa posteriorCovar posteriorMean priorCovar priorMean tau
views
Docs: confIgnored posteriorCovar posteriorMean priorCovar priorMean
tau views
Package: NADA Version: 1.5-2 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'boxplot-methods':
\S4method{boxplot}{ros}
Code: function(x, log = "y", range = 0, ...)
Docs: function(x, ...)
Argument names in code not in docs:
log range
Mismatches in argument names:
Position: 2 Code: log Docs: ...
Codoc mismatches from documentation object 'median-methods':
\S4method{median}{ros}
Code: function(x, na.rm = FALSE)
Docs: function(x, na.rm = FALSE, ...)
Argument names in docs not in code:
...
\S4method{median}{cenfit}
Code: function(x, na.rm = FALSE)
Docs: function(x, na.rm = FALSE, ...)
Argument names in docs not in code:
...
Codoc mismatches from documentation object 'predict-methods':
\S4method{predict}{cenfit}
Code: function(object, newdata, conf.int = FALSE)
Docs: function(object, newdata, conf.int = FALSE, ...)
Argument names in docs not in code:
...
\S4method{pexceed}{cenfit}
Code: function(object, newdata, conf.int = FALSE)
Docs: function(object, newdata, conf.int = FALSE, ...)
Argument names in docs not in code:
...
\S4method{pexceed}{ros}
Code: function(object, newdata, conf.int = FALSE, conf.level = 0.95)
Docs: function(object, newdata, conf.int = FALSE, ...)
Argument names in code not in docs:
conf.level
Argument names in docs not in code:
...
Mismatches in argument names:
Position: 4 Code: conf.level Docs: ...
Codoc mismatches from documentation object 'quantile-methods':
\S4method{quantile}{ros}
Code: function(x, probs = NADAprobs, ...)
Docs: function(object, probs = NADAprobs, ...)
Argument names in code not in docs:
x
Argument names in docs not in code:
object
Mismatches in argument names:
Position: 1 Code: x Docs: object
\S4method{quantile}{cenfit}
Code: function(x, probs = NADAprobs, conf.int = FALSE, ...)
Docs: function(object, probs = NADAprobs, conf.int = FALSE, ...)
Argument names in code not in docs:
x
Argument names in docs not in code:
object
Mismatches in argument names:
Position: 1 Code: x Docs: object
Codoc mismatches from documentation object 'summary-methods':
\S4method{summary}{ros}
Code: function(object, plot = FALSE, ...)
Docs: function(object, ...)
Argument names in code not in docs:
plot
Mismatches in argument names:
Position: 2 Code: plot Docs: ...
\S4method{summary}{cenfit}
Code: function(object, times, censored = FALSE, scale = 1, ...)
Docs: function(object, ...)
Argument names in code not in docs:
times censored scale
Mismatches in argument names:
Position: 2 Code: times Docs: ...
S4 class codoc mismatches from documentation object 'cenreg-class':
Slots for class 'cenreg'
Code: conf.int n n.cen survreg y ycen
Docs: survreg
S4 class codoc mismatches from documentation object 'summary.cenreg-class':
Slots for class 'summary.cenreg'
Code: .Data
Package: Ryacas Version: 0.2-9 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'runYacas':
runYacas
Code: function()
Docs: function(method = "system", yacas.args = "", yacas.init = "")
Argument names in docs not in code:
method yacas.args yacas.init
Package: SNPMaP Version: 1.0.2 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'SNPMaP-class':
\S4method{plot}{SNPMaP,missing}
Code: function(x, FUN = function(x) { x}, xlim = c(loX, hiX), ylim =
c(0, hiY), xlab = "guess", ylab = "Density", main =
"", col = rainbow(length(x at chps)), legend.position =
"left", legend.bty = "n", lty = 1:length(x at chps),
zero.line = TRUE, ...)
Docs: function(x, FUN = function(x) { x}, xlim = c(loX, hiX), ylim =
c(0, hiY), xlab = "guess", ylab = "Density", main =
x at table, col = rainbow(length(x at chps)),
legend.position = "left", legend.bty = "n", lty =
1:length(x at chps), zero.line = TRUE, ...)
Mismatches in argument default values:
Name: 'main' Code: "" Docs: x at table
\S4method{boxplot}{SNPMaP}
Code: function(x, FUN = function(x) { x}, ylab = "guess", main = "",
...)
Docs: function(x, FUN = function(x) { x}, ylab = "guess", main =
x at table, ...)
Mismatches in argument default values:
Name: 'main' Code: "" Docs: x at table
Package: TIMP Version: 1.8 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'amp-class':
Slots for class 'amp'
Code: C2 E2 amps autoclp0 chinde clinde clp0 clpCon clpType clpdep
clpequ clpequspec clpequspecBD cohcol compnames constrained
datCall datafile drel dscalspec fixed free fvecind getX
getXsuper highcon inten iter lclp0 lclpequ lowcon makeps mhist
mod_type mvecind ncomp nl nt nvecind outMat parnames
positivepar prel prelspec psi.df psi.weight pvecind satMat
scalx sigma simdata title usecompnames0 usecompnamesequ weight
weightList weightM weightpar weightsmooth x x2
Inherited: psi.df psi.weight x nt x2 nl C2 E2 sigma mod_type parnames
simdata weightpar weight weightM weightsmooth fixed clp0 makeps
clpequspec lclp0 lclpequ title mhist datCall dscalspec mvecind
drel clpequ scalx prel prelspec fvecind pvecind nvecind iter
free clpCon ncomp clpdep inten positivepar constrained clinde
chinde highcon lowcon datafile getX clpType clpequspecBD
compnames getXsuper usecompnames0 usecompnamesequ autoclp0
cohcol weightList outMat satMat
Docs: amp
S4 class codoc mismatches from documentation object 'dat-class':
Slots for class 'dat'
Code: C2 E2 autoclp0 chinde clinde clp0 clpCon clpType clpdep clpequ
clpequspec clpequspecBD cohcol compnames constrained datCall
datafile drel dscalspec fixed free fvecind getX getXsuper
highcon inten iter lclp0 lclpequ lowcon makeps mhist mod_type
mvecind ncomp nl nt nvecind outMat parnames positivepar prel
prelspec psi.df psi.weight pvecind satMat scalx sigma simdata
title usecompnames0 usecompnamesequ weight weightList weightM
weightpar weightsmooth x x2
Docs: C2 E2 autoclp0 clp0 clpCon clpType clpdep clpequ clpequspec
constrained datCall datafile drel drel dscalspec finished fixed
free fvecind groups inten iter lclp0 lclpequ makeps mhist
mod_type ncomp nl nt parnames positivepar prel prel prelspec
psi.df psi.weight pvecind scalx sigma simdata title weight
weightM weightpar weightsmooth x x2
S4 class codoc mismatches from documentation object 'fit-class':
Slots for class 'fit'
Code: nlsres resultlist rss
Docs: nlsres resultlist
S4 class codoc mismatches from documentation object 'kin-class':
Slots for class 'kin'
Code: C2 E2 amplitudes anipar anispec autoclp0 chinde clinde clp0
clpCon clpType clpdep clpequ clpequspec clpequspecBD coh cohcol
cohirf cohspec compnames constrained convalg datCall datafile
dispmu dispmufun disptau disptaufun doublegaus drel dscalspec
fixed fixedkmat free fullk fvecind getX getXsuper highcon
initialvals inten irf irffun irfpar iter jvec kin2scal kinpar
kinpar2 kinscal kinscalspecial kinscalspecialspec kmat kmatfit
lambdac lclp0 lclpequ lightregimespec lowcon makeps
measured_irf mhist mirf mod_type mvecind ncolc ncomp nl nt
numericalintegration nvecind outMat parmu parnames partau
positivepar prel prelspec psi.df psi.weight pvecind
reactantstoichiometrymatrix reftau satMat scalx seqmod sigma
simdata speckin2 specpar stoichiometrymatrix streak streakT
title usecompnames0 usecompnamesequ usekin2 wavedep weight
weightList weightM weightpar weightsmooth x x2
Inherited: psi.df psi.weight x nt x2 nl C2 E2 sigma mod_type parnames
simdata weightpar weight weightM weightsmooth fixed clp0 makeps
clpequspec lclp0 lclpequ title mhist datCall dscalspec mvecind
drel clpequ scalx prel prelspec fvecind pvecind nvecind iter
free clpCon ncomp clpdep inten positivepar constrained clinde
chinde highcon lowcon datafile getX clpType clpequspecBD
compnames getXsuper usecompnames0 usecompnamesequ autoclp0
cohcol weightList outMat satMat
Docs: amplitudes coh cohspec convalg dispmu dispmufun disptau
disptaufun doublegaus fullk initialvals irf irffun irfpar jvec
kinpar kinscal kmat kmatfit lambdac measured_irf mirf ncolc
numericalintegration parmu partau reactantstoichiometrymatrix
reftau seqmod specpar stoichiometrymatrix streak streakT
wavedep
S4 class codoc mismatches from documentation object 'kinopt-class':
Slots for class 'kinopt'
Code: FLIM FLIMresidimag adddataimage addest addfilename algorithm
breakdown coldata colfit divdrel getStartTri imagepal iter
kinspecerr kinspecest linrange ltydata ltyfit makeps maxfev
minFactor nlsalgorithm nnls nnlscrit noFLIMsummary noplotest
normspec notraces optimmethod output paropt parscale plot
plotcohcolspec plotkinspec plotpulsefol residplot residtraces
samespecline selectedtraces specinterpol specinterpolbspline
specinterpolpoints specinterpolseg stderrclp summaryplotcol
summaryplotrow sumnls superimpose title triStart trilinear
writeclperr writecon writedata writefit writefitivo
writenormspec writeplaincon writerawcon writespec
writespecinterpol xlab xlim xlimspec ylab ylimcomp ylimspec
ylimspecplus
Inherited: notraces residtraces selectedtraces writecon writespec
writenormspec writefit writefitivo writedata writeclperr
residplot plot minFactor output nnls divdrel noplotest
plotkinspec algorithm superimpose xlab ylab title makeps
linrange summaryplotrow summaryplotcol iter stderrclp trilinear
getStartTri triStart paropt addfilename addest adddataimage
kinspecerr xlimspec ylimspec ylimspecplus xlim specinterpol
specinterpolpoints specinterpolseg specinterpolbspline
samespecline normspec writespecinterpol nnlscrit nlsalgorithm
sumnls colfit coldata ltyfit ltydata optimmethod parscale
maxfev imagepal
Docs: FLIM: FLIMresidimag: breakdown kinspecest noFLIMsummary:
notraces plotcohcolspec plotpulsefol selectedtraces
writeplaincon writerawcon ylimcomp
S4 class codoc mismatches from documentation object 'multimodel-class':
Slots for class 'multimodel'
Code: algorithm data datasetind finished fit getXsuper groups
modeldiffs modellist modelspec nclp nnls nnlscrit optlist
parorder parorderchange parorderdiff stderrclp trilinear
Docs: data fit groups model modeldiffs modellist stderrclp
S4 class codoc mismatches from documentation object 'opt-class':
Slots for class 'opt'
Code: adddataimage addest addfilename algorithm coldata colfit
divdrel getStartTri imagepal iter kinspecerr linrange ltydata
ltyfit makeps maxfev minFactor nlsalgorithm nnls nnlscrit
noplotest normspec notraces optimmethod output paropt parscale
plot plotkinspec residplot residtraces samespecline
selectedtraces specinterpol specinterpolbspline
specinterpolpoints specinterpolseg stderrclp summaryplotcol
summaryplotrow sumnls superimpose title triStart trilinear
writeclperr writecon writedata writefit writefitivo
writenormspec writespec writespecinterpol xlab xlim xlimspec
ylab ylimspec ylimspecplus
Docs: adddataimage addest addfilename algorithm coldata colfit
divdrel iter kinspecerr linrange ltydata ltyfit makeps
nlsalgorithm nnls normspec output paropt plot plotkinspec
residplot samespecline specinterpol specinterpolbspline
specinterpolpoints specinterpolseg stderrclp summaryplotcol
summaryplotrow superimpose title writeclperr writecon writefit
writenormspec writespec writespecinterpol xlab xlimspec ylab
ylimspec ylimspecplus
S4 class codoc mismatches from documentation object 'res-class':
Slots for class 'res'
Code: cohirf cp fitted irfvec resid std_err_clp
Docs: cp fitted irfvec resid
S4 class codoc mismatches from documentation object 'theta-class':
Slots for class 'theta'
Code: amplitudes amps anipar clpequ coh cohirf drel irfpar jvec
kin2scal kinpar kinpar2 kinscal kinscalspecial parmu partau
peakpar prel shift specdisppar specpar
Docs: clpequ coh drel irfpar kinpar kinscal parmu partau prel
specdisppar specpar
Package: amba Version: 0.2.0 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'Estimation':
Estimation
Code: function()
Docs: function(...)
Argument names in docs not in code:
...
Package: backtest Version: 0.3-0 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'backtest-class':
Slots for class 'backtest'
Code: buckets by.period by.var date.var do.spread in.var natural
overlaps results ret.stats ret.var summary.stats turnover
Docs: buckets by.var date.var in.var natural rawstats results ret.var
Package: crosshybDetector Version: 1.0.4 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'AASequenceList-class':
Slots for class 'AASequenceList'
Code: .Data info names
Docs: .Data info
Package: fBasics Version: 2100.78 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'colorLocator':
colorMatrix
Code: function()
Docs: function(locator = TRUE)
Argument names in docs not in code:
locator
Package: fUtilities Version: 2100.77 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'colorLocator':
colorMatrix
Code: function()
Docs: function(locator = TRUE)
Argument names in docs not in code:
locator
Package: filehashSQLite Version: 0.2-2 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'filehashSQLite-class':
Slots for class 'filehashSQLite'
Code: datafile dbcon drv name
Inherited: name
Docs: datafile dbcon name
Package: grnnR Version: 1.0 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
Data sets with usage in documentation object 'P_trn' but not in code:
P_trn
Data sets with usage in documentation object 'P_tst' but not in code:
P_tst
Data sets with usage in documentation object 'T_trn' but not in code:
T_trn
Data sets with usage in documentation object 'T_tst' but not in code:
T_trn
Package: mmlcr Version: 1.3.5 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
Warning: file 'Srcdfull.rda' has magic number 'RDA1'
Use of save versions prior to 2 is deprecated
Package: nws Version: 1.7.0.0 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'nwsUseWs':
\S4method{nwsUseWs}{nwsServer}
Code: function(.Object, wsName, space = NULL, ...)
Docs: function(.Object, wsName, space = NULL)
Argument names in code not in docs:
...
S4 class codoc mismatches from documentation object 'netWorkSpace':
Slots for class 'netWorkSpace'
Code: cookieProtocol server wsName
Docs: server wsName
S4 class codoc mismatches from documentation object 'nwsServer':
Slots for class 'nwsServer'
Code: cookieProtocol nwsSocket port serverHost
Docs: nwsSocket port serverHost
S4 class codoc mismatches from documentation object 'sleighPending':
Slots for class 'sleighPending'
Code: accumulator barrierName numSubmitted numTasks nws sleighState
state
Docs: barrierName numTasks nws sleighState state
Package: portfolio Version: 0.4-4 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'matchedPortfolio-class':
Slots for class 'matchedPortfolio'
Code: formula matches method omitted.control omitted.treatment
original
Docs: formula matches original
S4 class codoc mismatches from documentation object 'tradelist-class':
Slots for class 'tradelist'
Code: actual candidates chunk.usd chunks chunks.actual data final
id.var mv.long.orig mv.short.orig price.var rank.gain.min
rank.sorts ranks regions restricted restrictions sorts swaps
swaps.actual target.equity tca to.equity trade.usd.min turnover
type unrestricted verbose
Docs: actual candidates chunk.usd chunks chunks.actual data final
id.var mv.long.orig mv.short.orig rank.sorts ranks regions
restricted restrictions sorts swaps swaps.actual target.equity
tca to.equity trade.usd.min turnover type unrestricted
Package: portfolioSim Version: 0.2-5 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'sdiDf-class':
Slots for class 'sdiDf'
Code: data
Docs: data period.var
S4 class codoc mismatches from documentation object 'stiFromSignal-class':
Slots for class 'stiFromSignal'
Code: chunk.usd equity in.var rebal.on sides size target
trading.style turnover type
Docs: equity in.var rebal.on sides size target trading.style type
Package: qualV Version: 0.2-4 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'compareME':
print.compareME
Code: function(x, ..., digits = 3)
Docs: function(object, ..., digits = 3)
Argument names in code not in docs:
x
Argument names in docs not in code:
object
Mismatches in argument names:
Position: 1 Code: x Docs: object
Package: race Version: 0.1.56 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
Functions/methods with usage in documentation object 'race.describe' but not in code:
race.describe
Functions/methods with usage in documentation object 'race.info' but not in code:
race.info
Functions/methods with usage in documentation object 'race.init' but not in code:
race.init
Functions/methods with usage in documentation object 'race.wrapper' but not in code:
race.wrapper
Package: tradeCosts Version: 0.3-0 Flavor: r-devel-linux-ix86
Check: for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'tradeCostsResults-class':
Slots for class 'tradeCostsResults'
Code: base.price batch.method batches benchmark.price executions
na.counts name
Docs: base.price batch.method benchmark.price na.counts name results
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