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 |
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