CRAN Package Check Results for Package ctsem

Last updated on 2021-04-11 05:47:52 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.4.2 1329.27 4.17 1333.44 ERROR --no-vignettes
r-devel-linux-x86_64-debian-gcc 3.4.2 787.97 207.90 995.87 NOTE --no-vignettes
r-devel-linux-x86_64-fedora-clang 3.4.2 2713.47 NOTE
r-devel-linux-x86_64-fedora-gcc 3.4.2 2209.48 NOTE
r-devel-windows-ix86+x86_64 3.4.2 666.00 297.00 963.00 NOTE --no-vignettes
r-devel-windows-x86_64-gcc10-UCRT 3.4.2 NOTE
r-patched-linux-x86_64 3.4.2 750.48 260.02 1010.50 NOTE --no-vignettes
r-patched-solaris-x86 3.4.2 2475.00 WARN
r-release-linux-x86_64 3.4.2 775.64 256.25 1031.89 NOTE --no-vignettes
r-release-macos-x86_64 3.4.2 NOTE
r-release-windows-ix86+x86_64 3.4.2 769.00 416.00 1185.00 NOTE --no-vignettes
r-oldrel-macos-x86_64 3.4.2 FAIL
r-oldrel-windows-ix86+x86_64 3.4.2 836.00 376.00 1212.00 NOTE --no-vignettes

Check Details

Version: 3.4.2
Flags: --no-vignettes
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-devel-linux-x86_64-debian-clang

Version: 3.4.2
Flags: --no-vignettes
Check: for GNU extensions in Makefiles
Result: NOTE
    GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 3.4.2
Check: installed package size
Result: NOTE
     installed size is 158.1Mb
     sub-directories of 1Mb or more:
     R 1.2Mb
     data 1.6Mb
     libs 154.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 3.4.2
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘pkgbuild’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-gcc10-UCRT, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 3.4.2
Check: for GNU extensions in Makefiles
Result: NOTE
    GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-gcc10-UCRT, r-patched-solaris-x86, r-release-macos-x86_64

Version: 3.4.2
Check: for detritus in the temp directory
Result: NOTE
    Found the following files/directories:
     ‘par-7269706c6579’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 3.4.2
Flags: --no-vignettes
Check: installed package size
Result: NOTE
     installed size is 9.8Mb
     sub-directories of 1Mb or more:
     R 1.2Mb
     data 1.6Mb
     libs 5.8Mb
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 3.4.2
Check: line endings in C/C++/Fortran sources/headers
Result: NOTE
    Found the following sources/headers with CR or CRLF line endings:
     src/stan_files/cov.hpp
     src/stan_files/ctsm.hpp
     src/stan_files/ctsmgen.hpp
    Some Unix compilers require LF line endings.
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 3.4.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘hierarchicalmanual.rnw’ using knitr
    System dimensions inferred from LAMBDA
    n.TDpred inferred inferred from TDpredNames
    n.TIpred inferred inferred from TIpredNames
    Custom par cint2 set as: param = cint2; transform = 10 * param; indvarying = TRUE; sdscale = 1; cint2 tipred effects from: TI1
    System dimensions inferred from manifestNames and latentNames
    n.TDpred inferred inferred from TDpredNames
    n.TIpred inferred inferred from TIpredNames
    LAMBDA vector spec input rowwise into 2 * 2 matrix:
    MANIFESTMEANS specified via single value -- filling 2 * 1 matrix:
    CINT vector spec input rowwise into 2 * 1 matrix:
    Custom par cint2 set as: param = cint2; transform = 10 * param; indvarying = TRUE; sdscale = 1; cint2 tipred effects from: TI1
    Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
    Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
    Maximum a posteriori estimation requested
    NA's in TIpreds - imputing 1 NA's to allow optimization -- TIpred effect estimates may be overly confident.
    NA's in TDpreds! Replaced by zeroes, consider appropriateness...
    Using 2/16 logical CPU cores
    starting worker pid=13782 on localhost:11543 at 07:13:30.836
    starting worker pid=13783 on localhost:11543 at 07:13:30.859
    Doing 1st pass with priors on reduced data set
    Loading required package: Rcpp
    Loading required package: Rcpp
    ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX')
    ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX')
    Optimizing...
    Including TI predictors...
    Estimating Hessian
    Computing posterior with 1000 samples
    Loading required package: data.table
    Loading required package: data.table
    Computing temporal regression coefficients for 100 samples, may take a moment...
    Fitting model to empty dataset...
    Maximum a posteriori estimation requested
    Using 1/16 logical CPU cores
    Optimizing...
    Estimating Hessian
    Computing posterior with 10000 samples
    Computing state estimates..
    Computing quantities for 1 samples...
    Getting 100 samples by 20 subjects for 2000 total samples
    Calculating time independent predictor effects...
    Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
    Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
    Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
    Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
    Custom par ma1 set as: param = ma1; transform = log(1+(exp(param))); indvarying = FALSE; sdscale = 1;
    Custom par a21 set as: param = a21; transform = -log(1+exp(param)); indvarying = FALSE; sdscale = 1;
    Custom par m1 set as: param = m1; transform = param*10+44; indvarying = TRUE; sdscale = 1;
    Bayesian estimation via Stan's NUTS sampler requested
    Individual variation not possible as only 1 subject! indvarying set to FALSE on all parameters
    Free T0VAR parameters fixed to diagonal matrix of 1 as only 1 subject - consider appropriateness!
    Setting DRIFT diagonals of 0 to approximate 0 of -0.000001
    Sampling...
    Warning: The largest R-hat is NA, indicating chains have not mixed.
    Running the chains for more iterations may help. See
    http://mc-stan.org/misc/warnings.html#r-hat
    Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
    Running the chains for more iterations may help. See
    http://mc-stan.org/misc/warnings.html#bulk-ess
    Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
    Running the chains for more iterations may help. See
    http://mc-stan.org/misc/warnings.html#tail-ess
    Error: processing vignette 'hierarchicalmanual.rnw' failed with diagnostics:
    Running 'texi2dvi' on 'hierarchicalmanual.tex' failed.
    Messages:
    /usr/local/bin/texi2dvi: line 365: 12470 Killed "$@" 2>&5 1>&2
    /usr/local/bin/texi2dvi: biber failed
    --- failed re-building ‘hierarchicalmanual.rnw’
    
    SUMMARY: processing the following file failed:
     ‘hierarchicalmanual.rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 3.4.2
Check: R code for possible problems
Result: FAIL
Flavor: r-oldrel-macos-x86_64