CRAN Package Check Results for Package ProFit

Last updated on 2019-03-27 00:48:10 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.6 47.12 132.93 180.05 OK
r-devel-linux-x86_64-debian-gcc 1.2.6 39.22 87.35 126.57 OK
r-devel-linux-x86_64-fedora-clang 1.2.6 196.07 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2.6 170.25 OK
r-devel-windows-ix86+x86_64 1.2.6 119.00 163.00 282.00 NOTE
r-patched-linux-x86_64 1.2.6 49.77 122.33 172.10 OK
r-patched-solaris-x86 1.2.6 244.40 NOTE
r-release-linux-x86_64 1.2.6 45.10 122.85 167.95 OK
r-release-windows-ix86+x86_64 1.2.6 116.00 159.00 275.00 NOTE
r-release-osx-x86_64 1.2.6 ERROR
r-oldrel-windows-ix86+x86_64 1.2.6 90.00 192.00 282.00 NOTE
r-oldrel-osx-x86_64 1.2.6 ERROR

Check Details

Version: 1.2.6
Check: installed package size
Result: NOTE
     installed size is 9.9Mb
     sub-directories of 1Mb or more:
     extdata 6.4Mb
     libs 2.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.2.6
Check: examples
Result: ERROR
    Running examples in ‘ProFit-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: profitSetupData
    > ### Title: Setup ProFit Data
    > ### Aliases: profitSetupData
    > ### Keywords: data
    >
    > ### ** Examples
    >
    > # Load ProFit example data
    >
    > # There are 2 data source options: KiDS or SDSS (the galaxies are the same)
    >
    > datasource='KiDS'
    >
    > # Now we can extract out the example files we have available for fitting by checking the
    > # contents of the directory containing the example FITS files:
    >
    > data('ExampleInit')
    > ExampleFiles=list.files(system.file("extdata",datasource,package="ProFit"))
    > ExampleIDs=unlist(strsplit(ExampleFiles[grep('fitim',ExampleFiles)],'fitim.fits'))
    > print(ExampleIDs)
     [1] "G265911" "G265940" "G266033" "G266035" "G266662" "G267199" "G267489"
     [8] "G267525" "G278109" "G279148"
    >
    > # There are 10 example galaxies included. Here we run example 1:
    >
    > useID=ExampleIDs[1]
    >
    > image = readFITS(system.file("extdata", paste(datasource,'/',useID,'fitim.fits',sep=''),
    + package="ProFit"))$imDat
    > sigma = readFITS(system.file("extdata", paste(datasource,'/',useID,'sigma.fits',sep=''),
    + package="ProFit"))$imDat
    > segim = readFITS(system.file("extdata", paste(datasource,'/',useID,'segim.fits',sep=''),
    + package="ProFit"))$imDat
    > psf = readFITS(system.file("extdata", paste(datasource,'/',useID,'psfim.fits',sep=''),
    + package="ProFit"))$imDat
    >
    > # Very rough model (not meant to look too good yet):
    >
    > useIDnum=as.integer(strsplit(useID,'G')[[1]][2])
    > useloc=which(ExampleInit$CATAID==useIDnum)
    >
    > # For our initial model we treat component 1 as the putitive bulge and componet 2 as
    > # the putitive disk. We are going to attempt a fit where the disk is forced to have
    > # nser=1 and the bulge has an axial ratio of 1.
    >
    > modellist=list(
    + sersic=list(
    + xcen= c(dim(image)[1]/2, dim(image)[1]/2),
    + ycen= c(dim(image)[2]/2, dim(image)[2]/2),
    + mag= c(ExampleInit$sersic.mag1[useloc], ExampleInit$sersic.mag2[useloc]),
    + re= c(ExampleInit$sersic.re1[useloc], ExampleInit$sersic.re2[useloc])*
    + if(datasource=='KiDS'){1}else{0.2/0.339},
    + nser= c(ExampleInit$sersic.nser1[useloc], 1), #Disk is initially nser=1
    + ang= c(ExampleInit$sersic.ang2[useloc], ExampleInit$sersic.ang2[useloc]),
    + axrat= c(1, ExampleInit$sersic.axrat2[useloc]), #Bulge is initially axrat=1
    + box=c(0, 0)
    + )
    + )
    >
    > # The pure model (no PSF):
    > magimage(profitMakeModel(modellist,dim=dim(image)))
    >
    > # The original image:
    > magimage(image)
    >
    > # The convolved model (with PSF):
    > magimage(profitMakeModel(modellist,dim=dim(image),psf=psf))
    >
    > # What should we be fitting:
    >
    > tofit=list(
    + sersic=list(
    + xcen= c(TRUE,NA), #We fit for xcen and tie the two together
    + ycen= c(TRUE,NA), #We fit for ycen and tie the two together
    + mag= c(TRUE,TRUE), #Fit for both
    + re= c(TRUE,TRUE), #Fit for both
    + nser= c(TRUE,FALSE), #Fit for bulge
    + ang= c(FALSE,TRUE), #Fit for disk
    + axrat= c(FALSE,TRUE), #Fit for disk
    + box= c(FALSE,FALSE) #Fit for neither
    + )
    + )
    >
    > # What parameters should be fitted in log space:
    >
    > tolog=list(
    + sersic=list(
    + xcen= c(FALSE,FALSE),
    + ycen= c(FALSE,FALSE),
    + mag= c(FALSE,FALSE),
    + re= c(TRUE,TRUE), #re is best fit in log space
    + nser= c(TRUE,TRUE), #nser is best fit in log space
    + ang= c(FALSE,FALSE),
    + axrat= c(TRUE,TRUE), #axrat is best fit in log space
    + box= c(FALSE,FALSE)
    + )
    + )
    >
    > # Setup the minimal data structure we need for likelihood.
    >
    > Data=profitSetupData(image=image, sigma=sigma, segim=segim, psf=psf,
    + modellist=modellist, tofit=tofit, tolog=tolog, magzero=0, algo.func='optim', verbose=TRUE)
    >
    > # Finally, calcualte the likelihood and make a plot:
    >
    > profitLikeModel(parm=Data$init, Data=Data, makeplots=TRUE)
    [1] "Summary of used sample:"
     Min. 1st Qu. Median Mean 3rd Qu. Max.
    -76.6588 -0.4123 0.4049 0.2498 1.2617 23.7657
    [1] "sd / 1-sig / 2-sig range:"
    [1] 3.558640 1.280227 4.606598
    [1] "Using 16777 out of 16777"
     sersic.xcen1 sersic.ycen1 sersic.mag1 sersic.mag2 sersic.re1
     8.4500e+01 9.3500e+01 1.6832e+01 1.6832e+01 8.4864e-01
     sersic.re2 sersic.nser1 sersic.ang2 sersic.axrat2
     1.1497e+00 6.4124e-01 1.4082e+02 -3.1060e-01 -1.2217e+05
    >
    > # If you're brave and your software/drivers are configured correctly, try benchmarking
    > # with OpenCL and OpenMP:
    > openclenvs = profitGetOpenCLEnvs(make.envs = TRUE)
    >
    > Data=profitSetupData(image=image, sigma=sigma, segim=segim, psf=psf,
    + modellist=modellist, tofit=tofit, tolog=tolog, magzero=0, algo.func='optim', verbose=TRUE,
    + nbenchmark = 5L, benchconvmethods = profitAvailableConvolvers(),
    + benchintmethods = profitAvailableIntegrators(), benchopenclenvs = openclenvs,
    + printbenchmark = TRUE, omp_threads=4)
     name env_name version dev_name
    1 brute <NA> NA <NA>
    2 opencl Apple 1.2 Intel(R) Xeon(R) CPU E5462 @ 2.80GHz
    3 opencl Apple 1.2 GeForce GT 630
     tinms.mean_single tinms.mean_double
    1 NA 7.8
    2 NA 47.0
    3 NA NA
    [1] "Best integrator: 'brute' device: 'NA', t=[7.80e+00 ms]"
     name env_name version dev_name
    1 brute <NA> NA <NA>
    2 opencl Apple 1.2 Intel(R) Xeon(R) CPU E5462 @ 2.80GHz
    3 opencl Apple 1.2 GeForce GT 630
    4 fftw <NA> NA <NA>
     tinms.mean_single tinms.mean_double
    1 NA 5.4
    2 NA 11.8
    3 NA NA
    4 NA 12.6
    [1] "Best convolver: 'brute' device: 'NA', t=[5.40e+00 ms]"
    >
    > profitLikeModel(parm=Data$init, Data=Data, makeplots=TRUE, plotchisq=TRUE)
     sersic.xcen1 sersic.ycen1 sersic.mag1 sersic.mag2 sersic.re1
     8.4500e+01 9.3500e+01 1.6832e+01 1.6832e+01 8.4864e-01
     sersic.re2 sersic.nser1 sersic.ang2 sersic.axrat2
     1.1497e+00 6.4124e-01 1.4082e+02 -3.1060e-01 -1.2217e+05
    >
    >
    >
    > ### * <FOOTER>
    > ###
    > cleanEx()
    > options(digits = 7L)
    > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
    Time elapsed: 11.322 1.364 11.122 0 0
    > grDevices::dev.off()
    null device
     1
    > ###
    > ### Local variables: ***
    > ### mode: outline-minor ***
    > ### outline-regexp: "\\(> \\)?### [*]+" ***
    > ### End: ***
    > quit('no')
    
     *** caught segfault ***
    address 0x60, cause 'memory not mapped'
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-release-osx-x86_64

Version: 1.2.6
Check: examples
Result: ERROR
    Running examples in ‘ProFit-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: profitSetupData
    > ### Title: Setup ProFit Data
    > ### Aliases: profitSetupData
    > ### Keywords: data
    >
    > ### ** Examples
    >
    > # Load ProFit example data
    >
    > # There are 2 data source options: KiDS or SDSS (the galaxies are the same)
    >
    > datasource='KiDS'
    >
    > # Now we can extract out the example files we have available for fitting by checking the
    > # contents of the directory containing the example FITS files:
    >
    > data('ExampleInit')
    > ExampleFiles=list.files(system.file("extdata",datasource,package="ProFit"))
    > ExampleIDs=unlist(strsplit(ExampleFiles[grep('fitim',ExampleFiles)],'fitim.fits'))
    > print(ExampleIDs)
     [1] "G265911" "G265940" "G266033" "G266035" "G266662" "G267199" "G267489"
     [8] "G267525" "G278109" "G279148"
    >
    > # There are 10 example galaxies included. Here we run example 1:
    >
    > useID=ExampleIDs[1]
    >
    > image = readFITS(system.file("extdata", paste(datasource,'/',useID,'fitim.fits',sep=''),
    + package="ProFit"))$imDat
    > sigma = readFITS(system.file("extdata", paste(datasource,'/',useID,'sigma.fits',sep=''),
    + package="ProFit"))$imDat
    > segim = readFITS(system.file("extdata", paste(datasource,'/',useID,'segim.fits',sep=''),
    + package="ProFit"))$imDat
    > psf = readFITS(system.file("extdata", paste(datasource,'/',useID,'psfim.fits',sep=''),
    + package="ProFit"))$imDat
    >
    > # Very rough model (not meant to look too good yet):
    >
    > useIDnum=as.integer(strsplit(useID,'G')[[1]][2])
    > useloc=which(ExampleInit$CATAID==useIDnum)
    >
    > # For our initial model we treat component 1 as the putitive bulge and componet 2 as
    > # the putitive disk. We are going to attempt a fit where the disk is forced to have
    > # nser=1 and the bulge has an axial ratio of 1.
    >
    > modellist=list(
    + sersic=list(
    + xcen= c(dim(image)[1]/2, dim(image)[1]/2),
    + ycen= c(dim(image)[2]/2, dim(image)[2]/2),
    + mag= c(ExampleInit$sersic.mag1[useloc], ExampleInit$sersic.mag2[useloc]),
    + re= c(ExampleInit$sersic.re1[useloc], ExampleInit$sersic.re2[useloc])*
    + if(datasource=='KiDS'){1}else{0.2/0.339},
    + nser= c(ExampleInit$sersic.nser1[useloc], 1), #Disk is initially nser=1
    + ang= c(ExampleInit$sersic.ang2[useloc], ExampleInit$sersic.ang2[useloc]),
    + axrat= c(1, ExampleInit$sersic.axrat2[useloc]), #Bulge is initially axrat=1
    + box=c(0, 0)
    + )
    + )
    >
    > # The pure model (no PSF):
    > magimage(profitMakeModel(modellist,dim=dim(image)))
    >
    > # The original image:
    > magimage(image)
    >
    > # The convolved model (with PSF):
    > magimage(profitMakeModel(modellist,dim=dim(image),psf=psf))
    >
    > # What should we be fitting:
    >
    > tofit=list(
    + sersic=list(
    + xcen= c(TRUE,NA), #We fit for xcen and tie the two together
    + ycen= c(TRUE,NA), #We fit for ycen and tie the two together
    + mag= c(TRUE,TRUE), #Fit for both
    + re= c(TRUE,TRUE), #Fit for both
    + nser= c(TRUE,FALSE), #Fit for bulge
    + ang= c(FALSE,TRUE), #Fit for disk
    + axrat= c(FALSE,TRUE), #Fit for disk
    + box= c(FALSE,FALSE) #Fit for neither
    + )
    + )
    >
    > # What parameters should be fitted in log space:
    >
    > tolog=list(
    + sersic=list(
    + xcen= c(FALSE,FALSE),
    + ycen= c(FALSE,FALSE),
    + mag= c(FALSE,FALSE),
    + re= c(TRUE,TRUE), #re is best fit in log space
    + nser= c(TRUE,TRUE), #nser is best fit in log space
    + ang= c(FALSE,FALSE),
    + axrat= c(TRUE,TRUE), #axrat is best fit in log space
    + box= c(FALSE,FALSE)
    + )
    + )
    >
    > # Setup the minimal data structure we need for likelihood.
    >
    > Data=profitSetupData(image=image, sigma=sigma, segim=segim, psf=psf,
    + modellist=modellist, tofit=tofit, tolog=tolog, magzero=0, algo.func='optim', verbose=TRUE)
    >
    > # Finally, calcualte the likelihood and make a plot:
    >
    > profitLikeModel(parm=Data$init, Data=Data, makeplots=TRUE)
    [1] "Summary of used sample:"
     Min. 1st Qu. Median Mean 3rd Qu. Max.
    -76.6588 -0.4123 0.4049 0.2498 1.2617 23.7657
    [1] "sd / 1-sig / 2-sig range:"
    [1] 3.558640 1.280227 4.606598
    [1] "Using 16777 out of 16777"
     sersic.xcen1 sersic.ycen1 sersic.mag1 sersic.mag2 sersic.re1
     8.4500e+01 9.3500e+01 1.6832e+01 1.6832e+01 8.4864e-01
     sersic.re2 sersic.nser1 sersic.ang2 sersic.axrat2
     1.1497e+00 6.4124e-01 1.4082e+02 -3.1060e-01 -1.2217e+05
    >
    > # If you're brave and your software/drivers are configured correctly, try benchmarking
    > # with OpenCL and OpenMP:
    > openclenvs = profitGetOpenCLEnvs(make.envs = TRUE)
    >
    > Data=profitSetupData(image=image, sigma=sigma, segim=segim, psf=psf,
    + modellist=modellist, tofit=tofit, tolog=tolog, magzero=0, algo.func='optim', verbose=TRUE,
    + nbenchmark = 5L, benchconvmethods = profitAvailableConvolvers(),
    + benchintmethods = profitAvailableIntegrators(), benchopenclenvs = openclenvs,
    + printbenchmark = TRUE, omp_threads=4)
     name env_name version dev_name
    1 brute <NA> NA <NA>
    2 opencl Apple 1.2 Intel(R) Xeon(R) CPU E5462 @ 2.80GHz
    3 opencl Apple 1.2 GeForce GT 630
     tinms.mean_single tinms.mean_double
    1 NA 11.2
    2 NA 46.2
    3 NA NA
    [1] "Best integrator: 'brute' device: 'NA', t=[1.12e+01 ms]"
     name env_name version dev_name
    1 brute <NA> NA <NA>
    2 opencl Apple 1.2 Intel(R) Xeon(R) CPU E5462 @ 2.80GHz
    3 opencl Apple 1.2 GeForce GT 630
    4 fftw <NA> NA <NA>
     tinms.mean_single tinms.mean_double
    1 NA 6.8
    2 NA 11.8
    3 NA NA
    4 NA 14.6
    [1] "Best convolver: 'brute' device: 'NA', t=[6.80e+00 ms]"
    >
    > profitLikeModel(parm=Data$init, Data=Data, makeplots=TRUE, plotchisq=TRUE)
     sersic.xcen1 sersic.ycen1 sersic.mag1 sersic.mag2 sersic.re1
     8.4500e+01 9.3500e+01 1.6832e+01 1.6832e+01 8.4864e-01
     sersic.re2 sersic.nser1 sersic.ang2 sersic.axrat2
     1.1497e+00 6.4124e-01 1.4082e+02 -3.1060e-01 -1.2217e+05
    >
    >
    >
    > ### * <FOOTER>
    > ###
    > options(digits = 7L)
    > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
    Time elapsed: 15.899 1.529 15.673 0.005 0.008
    > grDevices::dev.off()
    null device
     1
    > ###
    > ### Local variables: ***
    > ### mode: outline-minor ***
    > ### outline-regexp: "\\(> \\)?### [*]+" ***
    > ### End: ***
    > quit('no')
    
     *** caught segfault ***
    address 0x60, cause 'memory not mapped'
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-oldrel-osx-x86_64