CRAN Package Check Results for Package libamtrack

Last updated on 2014-04-19 11:48:53.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.5.4 5.65 24.11 29.76 NOTE
r-devel-linux-x86_64-debian-gcc 0.5.4 8.14 24.42 32.55 NOTE
r-devel-linux-x86_64-fedora-clang 0.5.4 57.19 NOTE
r-devel-linux-x86_64-fedora-gcc 0.5.4 58.50 NOTE
r-devel-macosx-x86_64-clang 0.5.4 50.53 NOTE
r-devel-macosx-x86_64-gcc 0.5.4 NOTE
r-devel-windows-ix86+x86_64 0.5.4 39.00 52.00 91.00 NOTE
r-patched-linux-x86_64 0.5.4 8.42 24.14 32.56 NOTE
r-patched-solaris-sparc 0.5.4 381.60 NOTE
r-patched-solaris-x86 0.5.4 94.90 NOTE
r-release-linux-ix86 0.5.4 18.00 45.00 63.00 NOTE
r-release-linux-x86_64 0.5.4 8.12 24.77 32.89 NOTE
r-release-windows-ix86+x86_64 0.5.4 50.00 51.00 101.00 NOTE
r-oldrel-windows-ix86+x86_64 0.5.4 41.00 58.00 99.00 NOTE

Check Details

Version: 0.5.4
Check: compilation flags in Makevars
Result: NOTE
    Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
    Installation with --no-configure' is unlikely to work. If you intended
    ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
    otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
    ‘cleanup’ script.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macosx-x86_64-clang, r-devel-macosx-x86_64-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.5.4
Check: Rd line widths
Result: NOTE
    Rd file 'AT.CPPSC.alpha.and.beta.Rd':
     \usage lines wider than 90 characters:
     AT.CPPSC.alpha.and.beta(E.MeV.u, particle.no, fluence.cm2.or.dose.Gy, material.no, RDD.model, RDD.parameters, ER.model, gamma.model, ga ... [TRUNCATED]
    
    Rd file 'AT.CSDA.energy.after.slab.E.MeV.u.Rd':
     \usage lines wider than 90 characters:
     AT.CSDA.energy.after.slab.E.MeV.u(E.initial.MeV.u, particle.no, material.no, slab.thickness.m)
    
    Rd file 'AT.CSDA.range.m.Rd':
     \examples lines wider than 100 characters:
     df <- expand.grid( particle.name = c("1H", "3He", "12C", "16O"), # Define parameter space:
     particle.energy.MeV.u = 10^seq(-1, 3, length.out = 500), # 1 nuclid, energy between 0.1 ... [TRUNCATED]
     df$CSDA.range.m[i] <- AT.CSDA.range.m( E.MeV.u = df$particle.energy.MeV.u[i],
     particle.no = AT.particle.no.from.particle.name(df$particle.name[i]),
     material.no = AT.material.no.from.material.name("Water, Liquid"))$CSDA.r ... [TRUNCATED]
     labels = c("1 um", "10 um", "0.1 mm", "1 mm", "1 cm", "10 cm", "1 m"),
     x = list( at = log10(c(.1, .3, 1, 3, 10, 30, 100, 300, 1000)),
     labels = c("0.1", "0.3", "1", "3", "10", "30", "100", "300", "1000"),
    
    Rd file 'AT.D.RDD.Gy.Rd':
     \examples lines wider than 100 characters:
     # Compute dose in several distances of an 100 MeV/u neon ion in water according to 'Site' parametrization
     df <- expand.grid( E.MeV.u = 10^seq(0, 3, length.out = 4), # from 1 to 1000 MeV/u in 4 steps
     r.m = 10^seq(-9, -2, length.out = 100), # from 1 nm to 1 cm in 100 steps
     rdd.model = 3, # Geiss parametrization
     rdd.parameter = 5e-8, # Fixed core size of 50 nm
     er.model = 4, # Geiss track width parametrization
     for (i in 1:nrow(df)){ # Loop through particles/energies
    
    Rd file 'AT.FLUKA.particle.name.to.libamtrack.particle.name.Rd':
     \examples lines wider than 100 characters:
     AT.FLUKA.particle.name.to.libamtrack.particle.name( FLUKA.particle.names = c("H*", "B*", "B10", "C12", "BE7", "U238") )
    
    Rd file 'AT.FLUKA.read.USRBIN.mesh.Rd':
     \usage lines wider than 90 characters:
     AT.FLUKA.read.USRBIN.mesh(exp.name, number.of.runs, unit, data.source = 'local', density.g.cm3 = 1.0)
    
    Rd file 'AT.FLUKA.read.USRBIN.regs.Rd':
     \usage lines wider than 90 characters:
     AT.FLUKA.read.USRBIN.regs(exp.name, number.of.runs, unit, data.source = 'local', vol.cm3 = NULL, density.g.cm3 = NULL)
    
    Rd file 'AT.FLUKA.read.USRTRACK.Rd':
     \usage lines wider than 90 characters:
     AT.FLUKA.read.USRTRACK(exp.name, number.of.runs, unit, data.source = 'local', compress = TRUE)
    
    Rd file 'AT.SPC.convert.to.DDD.Rd':
     \usage lines wider than 90 characters:
     AT.SPC.convert.to.DDD(file.name.spc, file.name.ddd = NULL, endian = 'little', plot = TRUE, write = TRUE, ...)
    
    Rd file 'AT.SPC.export.DEDX.Rd':
     \usage lines wider than 90 characters:
     AT.SPC.export.DEDX(stopping.power.source.no, file.name.DEDX = NULL, element.names = NULL, energy.MeV.u = NULL, plot = TRUE, write = TRU ... [TRUNCATED]
    
    Rd file 'AT.SPC.get.Rd':
     \examples lines wider than 100 characters:
     # # OF ONE KIND, i.e. same projectile, target, active/passive
    
    Rd file 'AT.SPC.get.list.Rd':
     \examples lines wider than 100 characters:
     # # OF ONE KIND, i.e. same projectile, target, active/passive
    
    Rd file 'AT.SPC.interpolate.Rd':
     \examples lines wider than 100 characters:
     # # OF ONE KIND, i.e. same projectile, target, active/passive
    
    Rd file 'AT.SPC.read.Rd':
     \examples lines wider than 100 characters:
     # # OF ONE KIND, i.e. same projectile, target, active/passive
    
    Rd file 'AT.Stopping.Power.Mass.Bethe.MeV.cm2.g.Rd':
     \usage lines wider than 90 characters:
     AT.Stopping.Power.Mass.Bethe.MeV.cm2.g(E.MeV.u, particle.no, material.no, E.restricted.keV)
    
    Rd file 'AT.beam.par.physical.to.technical.Rd':
     \examples lines wider than 100 characters:
     particle.no = AT.particle.no.from.particle.name("12C"), ... [TRUNCATED]
     material.no = AT.material.no.from.material.name("Water, ... [TRUNCATED]
     stopping.power.source.no = 0),
    
    Rd file 'AT.characteristic.single.scattering.angle.Rd':
     \usage lines wider than 90 characters:
     AT.characteristic.single.scattering.angle(E.MeV.u, particle.charge.e, target.thickness.cm, element.acronym)
    
    Rd file 'AT.characteristicple.scattering.angle.Rd':
     \usage lines wider than 90 characters:
     AT.characteristicple.scattering.angle(E.MeV.u, particle.charge.e, target.thickness.cm, element.acronym)
    
    Rd file 'AT.dose.Gy.from.fluence.cm2.Rd':
     \usage lines wider than 90 characters:
     AT.dose.Gy.from.fluence.cm2(E.MeV.u, particle.no, fluence.cm2, material.no, stopping.power.source.no)
    
    Rd file 'AT.dose.weighted.E.MeV.u.Rd':
     \usage lines wider than 90 characters:
     AT.dose.weighted.E.MeV.u(E.MeV.u, particle.no, fluence.cm2, material.no, stopping.power.source.no)
    
    Rd file 'AT.dose.weighted.LET.MeV.cm2.g.Rd':
     \usage lines wider than 90 characters:
     AT.dose.weighted.LET.MeV.cm2.g(E.MeV.u, particle.no, fluence.cm2, material.no, stopping.power.source.no)
    
    Rd file 'AT.effective.charge.from.E.MeV.u.Rd':
     \examples lines wider than 100 characters:
     particle.no = AT.particle.no.from.particle.name(df$particle.name[i])[1] ... [TRUNCATED]
    
    Rd file 'AT.effective.collision.number.Rd':
     \usage lines wider than 90 characters:
     AT.effective.collision.number(E.MeV.u, particle.charge.e, target.thickness.cm, element.acronym)
    
    Rd file 'AT.energy.straggling.after.slab.E.MeV.u.Rd':
     \usage lines wider than 90 characters:
     AT.energy.straggling.after.slab.E.MeV.u(E.MeV.u, particle.no, material.no, slab.thickness.m, initial.sigma.E.MeV.u)
    
    Rd file 'AT.fluence.cm2.from.dose.Gy.Rd':
     \usage lines wider than 90 characters:
     AT.fluence.cm2.from.dose.Gy(E.MeV.u, particle.no, D.Gy, material.no, stopping.power.source.no)
    
    Rd file 'AT.fluence.weighted.LET.MeV.cm2.g.Rd':
     \usage lines wider than 90 characters:
     AT.fluence.weighted.LET.MeV.cm2.g(E.MeV.u, particle.no, fluence.cm2, material.no, stopping.power.source.no)
    
    Rd file 'AT.gamma.response.Rd':
     \examples lines wider than 100 characters:
     d.Gy <- 10^seq(from = log10(0.1), to = log10(25), length.out = 100) # Compute 100 p ... [TRUNCATED]
     gamma.model <- 2 # General hit/t ... [TRUNCATED]
     R <- 1 # Probe ... [TRUNCATED]
     k2 = k2, D02 = 3.06, c2 = 2, m2 = 1,
     R <- 33 # Probe ... [TRUNCATED]
     k2 = k2, D02 = 1.77, c2 = 2, m2 = 1,
     R <- 13 # Probe ... [TRUNCATED]
     k2 = k2, D02 = 5.14, c2 = 2, m2 = 1,
     R <- 44 # Probe ... [TRUNCATED]
     k2 = k2, D02 = 4.66, c2 = 2, m2 = 1,
     ... [TRUNCATED]
     ... [TRUNCATED]
     lethal.event.mode = FALSE)$response
     ... [TRUNCATED]
     ... [TRUNCATED]
     lethal.event.mode = FALSE)$response
     ... [TRUNCATED]
     ... [TRUNCATED]
     lethal.event.mode = FALSE)$response
     ... [TRUNCATED]
     ... [TRUNCATED]
     lethal.event.mode = FALSE)$response
     df <- data.frame( d.Gy = rep( d.Gy, 4), # Compose data ... [TRUNCATED]
     S = c( vecA, vecB, vecC, vecD ),
     which = rep( c( rep("peak", length(d.Gy)),
     rep("total", length(d.G ... [TRUNCATED]
     probe = c( rep("probe A", 2 * length(d.Gy)),
     rep("probe B", 2 * length(d.Gy) ... [TRUNCATED]
    
     scales = list( x = list( at = log10(c(1,10,20)), labels = as.character(c(1,10,20))), y =list( at = c(4,5,6,7) ... [TRUNCATED]
    
    Rd file 'AT.material.no.from.material.name.Rd':
     \examples lines wider than 100 characters:
     AT.material.no.from.material.name( material.name = c("Water, Liquid", "PMMA", "Squirrel liver pudding"))
    
    Rd file 'AT.max.E.transfer.MeV.Rd':
     \examples lines wider than 100 characters:
     max.E.keV.classical = AT.max.E.transfer.MeV(-1.0 * E.MeV.u)$max.E.transfer.MeV * 1000,
     max.E.keV.relativistic = AT.max.E.transfer.MeV(E.MeV.u)$max.E.transfer.MeV * 1000)
     scales = list( x = list( at = 0:3, labels = c("1 MeV/u", "10 MeV/u", "100 MeV/u", "1 GeV/u")),
    
    Rd file 'AT.mean.number.of.tracks.contrib.Rd':
     \usage lines wider than 90 characters:
     AT.mean.number.of.tracks.contrib(E.MeV.u, particle.no, fluence.cm2, material.no, er.model,
    
    Rd file 'AT.momentum.MeV.c.u.from.E.MeV.u.Rd':
     \examples lines wider than 100 characters:
     p.MeV.c = AT.momentum.MeV.c.u.from.E.MeV.u(E.MeV.u)$momentum.MeV.c)
    
    Rd file 'AT.reduced.target.thickness.Rd':
     \usage lines wider than 90 characters:
     AT.reduced.target.thickness(E.MeV.u, particle.charge.e, target.thickness.cm, element.acronym)
    
    Rd file 'AT.run.CPPSC.method.Rd':
     \usage lines wider than 90 characters:
     AT.run.CPPSC.method(E.MeV.u, particle.no, fluence.cm2.or.dose.Gy, material.no, stopping.power.source.no,
     \examples lines wider than 100 characters:
     AT.run.CPPSC.method( particle.no = c(6012, 1001, 1001), # namely carbon, protons, and protons with
     E.MeV.u = c(270, 270, 5), # 270 MeV/u (primary Carbon, 270 MeV/u and 5 M ... [TRUNCATED]
     fluence.cm2.or.dose.Gy = c(1e8, 1e9, 1e7), # and their corresponding fluences
     material.no = 5, # i.e. Alanine
     rdd.model = 3, # simple 'Geiss' parametrization of radial dos ... [TRUNCATED]
     rdd.parameter = 50e-9, # with 50 nm core radius
     er.model = 4, # M. Scholz' parametrization of track radius
     gamma.model = 2, # General hit/target X ray response, but
     gamma.parameters = c(1,500,1,1,0), # as simple single exponential saturation (one ... [TRUNCATED]
     N2 = 10, # ten bins per factor 2 for internal local dos ... [TRUNCATED]
     fluence.factor = 1.0, # can be used to easily scale total fluence (h ... [TRUNCATED]
     write.output = TRUE, # write a log file
     shrink.tails = TRUE, # cut tails of local dose distribution, if...
     shrink.tails.under = 1e-30, # ... they contribute less then 1e-30 to first ... [TRUNCATED]
     adjust.N2 = TRUE, # perform rebinning if local dose distribution ... [TRUNCATED]
     lethal.events.mode = FALSE, # use independent subtargets
    
    Rd file 'AT.run.GSM.method.Rd':
     \usage lines wider than 90 characters:
     AT.run.GSM.method(E.MeV.u, particle.no, fluence.cm2.or.dose.Gy, material.no, stopping.power.source.no,
     \examples lines wider than 100 characters:
     AT.run.GSM.method( particle.no = 1001, # protons with
     fluence.cm2.or.dose.Gy = c(-1.0), # delivering 1 Gy
     material.no = 5, # i.e. Alanine
     rdd.model = 3, # simple 'Geiss' parametrization of radial dose ... [TRUNCATED]
     rdd.parameter = 50e-9, # with 50 nm core radius
     er.model = 4, # M. Scholz' parametrization of track radius
     gamma.model = 4, # Use exponential saturation
     gamma.parameters = c(1,500), # max. response normalized to 1, saturation dose ... [TRUNCATED]
     N.runs = 1000, # resample 1000 times
     write.output = TRUE, # write a log file
     nX = 10, # use a 10x10 grid
     voxel.size.m = 5e-9, # with 5 nm voxel size
     lethal.events.mode = FALSE, # use independent subtargets
    
    Rd file 'AT.run.IGK.method.Rd':
     \usage lines wider than 90 characters:
     AT.run.IGK.method(E.MeV.u, particle.no, fluence.cm2.or.dose.Gy, material.no, stopping.power.source.no,
     \examples lines wider than 100 characters:
     AT.run.IGK.method( particle.no = 1001, # namely protons with
     fluence.cm2.or.dose.Gy = c(-1.0), # delivering 1 Gy
     material.no = 5, # i.e. Alanine
     rdd.model = 4, # Katz parametrization of radial dose distributi ... [TRUNCATED]
     rdd.parameter = c(5e-8,1e-10), # with 50 nm target size and 1e-10 dose minimum
     er.model = 2, # Butts&Katz parametrization of track radius
     gamma.model = 2, # Use general target/hit model but here...
     gamma.parameters = c(1,500,1,1,0), # ...as exponential saturation with characterist ... [TRUNCATED]
     saturation.cross.section.factor = 1.4, # factor to take 'brush' around track into accou ... [TRUNCATED]
     write.output = TRUE, # write a log file
    
    Rd file 'AT.scattering.angle.distribution.Rd':
     \usage lines wider than 90 characters:
     AT.scattering.angle.distribution(E.MeV.u, particle.charge.e, target.thickness.cm, element.acronym, Theta)
    
    Rd file 'AT.stopping.power.ratio.Rd':
     \usage lines wider than 90 characters:
     AT.stopping.power.ratio(E.MeV.u, particle.no, fluence.cm2, material.no, reference.material.no,
     \examples lines wider than 100 characters:
     df <- expand.grid( particle.name = "1H", # Define parameter space:
     particle.energy.MeV.u = 10^seq(-1, 3, length.out = 500), # 1 nuclid, energy between 0.1 ... [TRUNCATED]
     material.name = c("Air", "PMMA", "Aluminum Oxide"), # and three materials
     df$stopping.power.ratio[i] <- AT.stopping.power.ratio( E.MeV.u = df$particle.energy.MeV.u[i],
     particle.no = df$particle.no[i],
     fluence.cm2 = 1, # does not have any mea ... [TRUNCATED]
     material.no = df$material.no[i],
     reference.material.no = material.no.water,
    
    Rd file 'libamtrack-package.Rd':
     \examples lines wider than 100 characters:
     df <- expand.grid( E.MeV.u = 10^seq(0, 3, length.out = 4), # from 1 to 1000 MeV/u in 4 steps
     particle.no = c(1001,6012), # protons and carbons
     r.m = 10^seq(-9, -2, length.out = 100), # from 1 nm to 1 cm in 100 steps
     material.no = 2, # Aluminium Oxide
     rdd.model = 3, # Geiss parametrization
     rdd.parameter = 5e-8, # Fixed core size of 50 nm
     er.model = 4, # Geiss track width parametrization
     ii <- df$particle.no == 1001 # Add particle names
     for (i in 1:nrow(df)){ # Loop through particles/energies
     stopping.power.source.no = 0)[[1]] # use PSTAR data
     AT.run.IGK.method( particle.no = 1001, # namely protons with
     fluence.cm2.or.dose.Gy = c(-1.0), # delivering 1 Gy
     material.no = 5, # i.e. Alanine
     rdd.model = 4, # Katz parametrization of radial dose distributi ... [TRUNCATED]
     rdd.parameter = c(5e-8,1e-10), # with 50 nm target size and 1e-10 dose minimum
     er.model = 2, # Butts&Katz parametrization of track radius
     gamma.model = 2, # Use general target/hit model but here...
     gamma.parameters = c(1,500,1,1,0), # ...as exponential saturation with characterist ... [TRUNCATED]
     saturation.cross.section.factor = 1.4, # factor to take 'brush' around track into accou ... [TRUNCATED]
     write.output = TRUE, # write a log file
     stopping.power.source.no = 0) # use PSTAR data
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc