• using R version 2.11.0 Under development (unstable) (2010-01-14 r50981)
• using session charset: UTF-8
• checking for file 'TIMP/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'TIMP' version '1.8'
• checking package name space information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking for executable files ... OK
• checking whether package 'TIMP' can be installed ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the name space can be loaded with stated dependencies ... OK
• checking whether the name space can be unloaded cleanly ... OK
• checking for unstated dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking 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
  
• checking Rd \usage sections ... OK
• checking data for non-ASCII characters ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable use of $BLAS_LIBS ... OK
• checking examples ... OK
• checking tests ... OK
• checking PDF version of manual ... OK