* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/panglm.Rcheck’
* using R Under development (unstable) (2026-11-03 r90835)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.2.1 20261029 (Red Hat 16.2.1-3)
    GNU Fortran (GCC) 16.2.1 20261029 (Red Hat 16.2.1-3)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-11-04 04:35:57 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘panglm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘panglm’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘panglm’ can be installed ... [127s/263s] OK
* used C++ compiler: ‘g++ (GCC) 16.2.1 20261029 (Red Hat 16.2.1-3)’
* checking C++ specification ... INFO
  specified C++17
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [40s/66s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [176s/224s]
 [176s/224s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(panglm)
  > 
  > test_check("panglm")
  17 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  17 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  26 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  6 group(s) whose positive counts are all 1 dropped from the count part -- their intercept is not finite and they carry no information.
  26 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  6 group(s) whose positive counts are all 1 dropped from the count part -- their intercept is not finite and they carry no information.
  26 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  6 group(s) whose positive counts are all 1 dropped from the count part -- their intercept is not finite and they carry no information.
  26 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  6 group(s) whose positive counts are all 1 dropped from the count part -- their intercept is not finite and they carry no information.
  37 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  NOTE: 1 fixed-effect (5 observations) removed because of only 0 outcomes or singletons.
  17 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  Saving _problems/test-fmm-86.R
  21 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  11 group(s) whose positive counts are all 1 dropped from the count part -- their intercept is not finite and they carry no information.
  12 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  
  warning: solve(): system is singular; attempting approx solution
  
  warning: solve(): system is singular; attempting approx solution
  
  warning: solve(): system is singular; attempting approx solution
  
  warning: solve(): system is singular; attempting approx solution
  
  warning: solve(): system is close to singular; rcond: 4.01387e-17; attempting approx solution
  17 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  26 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  6 group(s) whose positive counts are all 1 dropped from the count part -- their intercept is not finite and they carry no information.
  
  warning: solve(): system is singular; attempting approx solution
  
  warning: solve(): system is singular; attempting approx solution
  17 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  17 group(s) with no within-group outcome variation dropped (all-0 or all-1) -- they carry no information for the conditional likelihood.
  Saving _problems/test-qr-96.R
  Saving _problems/test-qr-156.R
  Saving _problems/test-qr-166.R
  Saving _problems/test-qr-169.R
  
  warning: solve(): system is singular; attempting approx solution
  
  warning: solve(): system is singular; attempting approx solution
  Saving _problems/test-select-90.R
  2 group(s) with all-zero outcomes dropped -- their fixed effect is unbounded under the dummy-variable NB2 MLE and carries no information about the shared slope.
  [ FAIL 6 | WARN 3 | SKIP 15 | PASS 2240 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • On CRAN (15): 'test-gamma.R:39:3', 'test-hurdle.R:167:3',
    'test-model-frame.R:176:3', 'test-ordered.R:31:3', 'test-ordered.R:44:3',
    'test-qr.R:79:3', 'test-random.R:84:3', 'test-random.R:99:3',
    'test-select.R:104:3', 'test-slopes.R:71:3', 'test-slopes.R:91:3',
    'test-slopes.R:116:3', 'test-slopes.R:173:3', 'test-twopart-cre.R:62:3',
    'test-twopart-cre.R:117:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fmm.R:86:3'): methods: predict, summary, cluster vcov, seed, panfmmselect ──
  Expected `coef(a)` to be identical to `coef(b)`.
  Differences:
    `actual`: -0.4491443426 0.2522890209 1.4531670267 0.5577073525 -0.4091845806
  `expected`: -0.4491443401 0.2522890240 1.4531670313 0.5577073490 -0.4091845738
  
  ── Failure ('test-qr.R:96:3'): cluster bootstrap is reproducible and close to the analytic SE ──
  Expected `vcov(b1)` to be identical to `vcov(b2)`.
  Differences:
      actual                  | expected                   
  [1] 0.01770947830352131644  - 0.01770947830352132338  [1]
  [2] -0.00315823100973720503 - -0.00315823100973720459 [2]
  [3] -0.01122849260704015736 | -0.01122849260704015736 [3]
  [4] -0.00315823100973720503 - -0.00315823100973720459 [4]
  [5] 0.00704628402437314314  | 0.00704628402437314314  [5]
  [6] 0.00466580852029690497  - 0.00466580852029690584  [6]
  [7] -0.01122849260704015736 | -0.01122849260704015736 [7]
  [8] 0.00466580852029690497  - 0.00466580852029690584  [8]
  [9] 0.02126887041653793484  - 0.02126887041653793137  [9]
  
  ── Failure ('test-qr.R:156:3'): panqr() takes boot and seed; R is a deprecated alias of boot ──
  Expected `vcov(a)` to be identical to `vcov(b)`.
  Differences:
      actual                 | expected                  
  [1] 0.0573548056328181607  - 0.0573548056328181538  [1]
  [2] 0.0074753139383377980  - 0.0074753139383377945  [2]
  [3] -0.0248846178250003054 - -0.0248846178250002985 [3]
  [4] 0.0074753139383377980  - 0.0074753139383377945  [4]
  [5] 0.0046797877162826126  - 0.0046797877162826039  [5]
  [6] -0.0046890500493214256 - -0.0046890500493214204 [6]
  [7] -0.0248846178250003054 - -0.0248846178250002985 [7]
  [8] -0.0046890500493214256 - -0.0046890500493214204 [8]
  [9] 0.0274420652411665016  - 0.0274420652411664946  [9]
  
  ── Failure ('test-qr.R:166:3'): panqr() takes boot and seed; R is a deprecated alias of boot ──
  Expected `vcov(s1)` to be identical to `vcov(s2)`.
  Differences:
      actual                 | expected                  
  [1] 0.0379799121480062646  - 0.0379799121480062785  [1]
  [2] 0.0053219215616325984  - 0.0053219215616325949  [2]
  [3] -0.0131765663158094262 - -0.0131765663158094279 [3]
  [4] 0.0053219215616325984  - 0.0053219215616325949  [4]
  [5] 0.0074040011755511816  | 0.0074040011755511816  [5]
  [6] -0.0047183668308177253 - -0.0047183668308177235 [6]
  [7] -0.0131765663158094262 - -0.0131765663158094279 [7]
  [8] -0.0047183668308177253 - -0.0047183668308177235 [8]
  [9] 0.0147702764043608336  | 0.0147702764043608336  [9]
  
  ── Failure ('test-qr.R:169:3'): panqr() takes boot and seed; R is a deprecated alias of boot ──
  Expected `vcov(s1)` to be identical to `vcov(s3)`.
  Differences:
      actual                  | expected                   
  [1] 0.03797991214800626458  | 0.03797991214800626458  [1]
  [2] 0.00532192156163259836  - 0.00532192156163259922  [2]
  [3] -0.01317656631580942615 | -0.01317656631580942615 [3]
  [4] 0.00532192156163259836  - 0.00532192156163259922  [4]
  [5] 0.00740400117555118156  | 0.00740400117555118156  [5]
  [6] -0.00471836683081772526 - -0.00471836683081772613 [6]
  [7] -0.01317656631580942615 | -0.01317656631580942615 [7]
  [8] -0.00471836683081772526 - -0.00471836683081772613 [8]
  [9] 0.01477027640436083360  - 0.01477027640436083533  [9]
  
  ── Failure ('test-select.R:90:3'): the panel bootstrap is reproducible and leaves the RNG state alone ──
  Expected `vcov(f1)` to be identical to `vcov(f2)`.
  Differences:
       actual                 | expected                              
   [1] 0.00625291025869165185 - 0.00625291025869165878 [1]            
   [2] 0.00213512497734625641 - 0.00213512497734627158 [2]            
   [3] 0.00206292959608664816 - 0.00206292959608664903 [3]            
   [4] 0.00897238439866607576 - 0.00897238439866606709 [4]            
   [5] 0.01347193873298600277 - 0.01347193873298601838 [5]            
   [6] 0.00213512497734625641 - 0.00213512497734627158 [6]            
   [7] 0.11813034895270908831 - 0.11813034895270911606 [7]            
   [8] 0.01406309581948395407 - 0.01406309581948398009 [8]            
   [9] 0.03096856004375564408 - 0.03096856004375572388 [9]            
  [10] 0.00191520655699730724 - 0.00191520655699730247 [10]           
   ... ...                      ...                    and 15 more ...
  
  
  [ FAIL 6 | WARN 3 | SKIP 15 | PASS 2240 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [37s/38s] OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/localhost/ripley/R/packages/tests-MKL/panglm.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 11:21.77, 415.69 + 22.98