SPSS Statistics

SPSS Statistics

Your hub for statistical analysis, data management, and data documentation. Connect, learn, and share with your peers! 

 View Only

  • 1.  Firth logistic extension - "logistf package is required but could not be loaded"

    Posted Tue September 17, 2024 03:38 PM

    Hi,

    I am trying to install the SPSS extension to do the firth logistic regression analysis (see github link below) and am getting the error message "logistf package is required but could not be loaded. I have SPSS 27 and have downloaded R version 3.6.0 and have tried to install STATS_R36_configuration.

    I have pasted below the output I get in SPSS and the output I get in R when I try and install logistf in R.

    There is another string of messages in this forum where someone had a similar problem however they found another way to do the analysis and so the problem was never resolved.

    If anyone can help it would be much appreciated! Thanks!

    Anne

    https://github.com/IBMPredictiveAnalytics/STATS_FIRTHLOG


    > install.packages("logistf")
    Installing package into 'C:/Users/anne_sonley/Documents/R/win-library/3.6'
    (as 'lib' is unspecified)
    --- Please select a CRAN mirror for use in this session ---
    also installing the dependencies 'bit', 'bit64', 'progress', 'minqa', 'nloptr', 'ucminf', 'vroom', 'tzdb', 'stringi', 'fansi', 'utf8', 'lme4', 'ordinal', 'forcats', 'hms', 'readr', 'backports', 'glue', 'lifecycle', 'purrr', 'stringr', 'tibble', 'cli', 'magrittr', 'pillar', 'tidyselect', 'vctrs', 'RcppEigen', 'pan', 'jomo', 'haven', 'broom', 'dplyr', 'glmnet', 'mitml', 'Rcpp', 'rlang', 'tidyr', 'mice'

    Warning: unable to access index for repository https://mirror.csclub.uwaterloo.ca/CRAN/bin/windows/contrib/3.6:
      cannot open URL 'https://mirror.csclub.uwaterloo.ca/CRAN/bin/windows/contrib/3.6/PACKAGES'
    Packages which are only available in source form, and may need
      compilation of C/C++/Fortran: 'bit' 'bit64' 'minqa' 'nloptr' 'ucminf'
      'vroom' 'tzdb' 'stringi' 'fansi' 'utf8' 'lme4' 'ordinal' 'readr'
      'backports' 'glue' 'purrr' 'tibble' 'cli' 'magrittr' 'tidyselect'
      'vctrs' 'RcppEigen' 'pan' 'jomo' 'haven' 'dplyr' 'glmnet' 'Rcpp'
      'rlang' 'tidyr' 'mice' 'logistf'
      These will not be installed
    installing the source packages 'progress', 'forcats', 'hms', 'lifecycle', 'stringr', 'pillar', 'broom', 'mitml'

    trying URL 'https://mirror.csclub.uwaterloo.ca/CRAN/src/contrib/progress_1.2.3.tar.gz'
    Content type 'text/plain' length 30499 bytes (29 KB)
    downloaded 29 KB

    trying URL 'https://mirror.csclub.uwaterloo.ca/CRAN/src/contrib/forcats_1.0.0.tar.gz'
    Content type 'text/plain' length 294183 bytes (287 KB)
    downloaded 287 KB

    trying URL 'https://mirror.csclub.uwaterloo.ca/CRAN/src/contrib/hms_1.1.3.tar.gz'
    Content type 'text/plain' length 43379 bytes (42 KB)
    downloaded 42 KB

    trying URL 'https://mirror.csclub.uwaterloo.ca/CRAN/src/contrib/lifecycle_1.0.4.tar.gz'
    Content type 'text/plain' length 107656 bytes (105 KB)
    downloaded 105 KB

    trying URL 'https://mirror.csclub.uwaterloo.ca/CRAN/src/contrib/stringr_1.5.1.tar.gz'
    Content type 'text/plain' length 176599 bytes (172 KB)
    downloaded 172 KB

    trying URL 'https://mirror.csclub.uwaterloo.ca/CRAN/src/contrib/pillar_1.9.0.tar.gz'
    Content type 'text/plain' length 444528 bytes (434 KB)
    downloaded 434 KB

    trying URL 'https://mirror.csclub.uwaterloo.ca/CRAN/src/contrib/broom_1.0.6.tar.gz'
    Content type 'text/plain' length 641538 bytes (626 KB)
    downloaded 626 KB

    trying URL 'https://mirror.csclub.uwaterloo.ca/CRAN/src/contrib/mitml_0.4-5.tar.gz'
    Content type 'text/plain' length 223835 bytes (218 KB)
    downloaded 218 KB

    ERROR: dependencies 'cli', 'glue', 'rlang' are not available for package 'lifecycle'
    * removing 'C:/Users/anne_sonley/Documents/R/win-library/3.6/lifecycle'
    ERROR: dependencies 'pan', 'jomo', 'haven' are not available for package 'mitml'
    * removing 'C:/Users/anne_sonley/Documents/R/win-library/3.6/mitml'
    ERROR: dependencies 'cli', 'glue', 'lifecycle', 'magrittr', 'rlang', 'tibble' are not available for package 'forcats'
    * removing 'C:/Users/anne_sonley/Documents/R/win-library/3.6/forcats'
    ERROR: dependencies 'lifecycle', 'rlang', 'vctrs' are not available for package 'hms'
    * removing 'C:/Users/anne_sonley/Documents/R/win-library/3.6/hms'
    ERROR: dependencies 'cli', 'glue', 'lifecycle', 'magrittr', 'rlang', 'stringi', 'vctrs' are not available for package 'stringr'
    * removing 'C:/Users/anne_sonley/Documents/R/win-library/3.6/stringr'
    ERROR: dependencies 'cli', 'fansi', 'glue', 'lifecycle', 'rlang', 'utf8', 'vctrs' are not available for package 'pillar'
    * removing 'C:/Users/anne_sonley/Documents/R/win-library/3.6/pillar'
    ERROR: dependency 'hms' is not available for package 'progress'
    * removing 'C:/Users/anne_sonley/Documents/R/win-library/3.6/progress'
    ERROR: dependencies 'backports', 'dplyr', 'glue', 'lifecycle', 'purrr', 'rlang', 'stringr', 'tibble', 'tidyr' are not available for package 'broom'
    * removing 'C:/Users/anne_sonley/Documents/R/win-library/3.6/broom'

    The downloaded source packages are in
            'C:\Users\anne_sonley\AppData\Local\Temp\RtmpSiRUl5\downloaded_packages'
    Warning messages:
    1: In install.packages("logistf") :
      installation of package 'lifecycle' had non-zero exit status
    2: In install.packages("logistf") :
      installation of package 'mitml' had non-zero exit status
    3: In install.packages("logistf") :
      installation of package 'forcats' had non-zero exit status
    4: In install.packages("logistf") :
      installation of package 'hms' had non-zero exit status
    5: In install.packages("logistf") :
      installation of package 'stringr' had non-zero exit status
    6: In install.packages("logistf") :
      installation of package 'pillar' had non-zero exit status
    7: In install.packages("logistf") :
      installation of package 'progress' had non-zero exit status
    8: In install.packages("logistf") :
      installation of package 'broom' had non-zero exit status
    > 



    ------------------------------
    Anne Sonley
    ------------------------------


  • 2.  RE: Firth logistic extension - "logistf package is required but could not be loaded"
    Best Answer

    Posted Tue September 17, 2024 03:49 PM
    That package should have been installed when you installed the extension command.  Sometimes this fails due to internet problems or permissions issues.

    Try this.
    Install the STATS PACKAGE INSTALL extension command via Extensions > Extension Hub.
    Run that procedure, which will appear on the Extensions menu, and specify logistf.
    If it fails, it may give an error message that can help to diagnose the problem.

    --



    Original Message


  • 3.  RE: Firth logistic extension - "logistf package is required but could not be loaded"

    Posted Fri September 20, 2024 12:16 PM

    Hi Jon,

    Thank you very much for you help! By following your instructions above it now seems to have been installed!

    Anne



    ------------------------------
    Anne Sonley
    ------------------------------

    Original Message


  • 4.  RE: Firth logistic extension - "logistf package is required but could not be loaded"

    Posted Fri September 20, 2024 03:16 PM

    Oh shoot, I spoke to soon. The program seems to be installed but now I am getting the error message

    >Warning # 6894. Command name: BEGIN PROGRAM

    >The external program exited unexpectedly and lost its content, a new external

    >program will startup to execute the rest of the job.

    And then nothing happens after that. Other threads I have read with regards to this error message seem to be related to python not R. 

    Aldo if this is not the correct place to post about this and I should start a new thread please let me know. 

    Thanks!

    Anne



    ------------------------------
    Anne Sonley
    ------------------------------

    Original Message


  • 5.  RE: Firth logistic extension - "logistf package is required but could not be loaded"

    Posted Fri September 20, 2024 03:25 PM
    This would be an R issue, not a Python issue.

    Try running a really simple equation to see whether it is always happening with this procedure.  Also try some other R-based procedure. For example, STATS RELIMP (Analyze > Regression > Regression Relative Importance).  You would need to install that from the Extension Hub.

    If you can send me the data and syntax (jkpeck@gmail.com), I can take a look.

    --



    Original Message