* using log directory ‘/srv/hornik/tmp/CRAN/eDNAjoint.Rcheck’
* using R Under development (unstable) (2023-08-28 r85029)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (10)
    GNU Fortran (Debian 13.2.0-1) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘eDNAjoint/DESCRIPTION’ ... OK
* this is package ‘eDNAjoint’ version ‘0.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Abigail G. Keller <agkeller@berkeley.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  catchability (8:557)
  eDNA (8:50, 8:261, 8:437, 8:507)
  electrofishing (8:222)
  nondetection (8:276)
  polymerase (8:298)
  qPCR (8:338)

Found the following (possibly) invalid file URI:
  URI: doi.org/10.6084/m9.figshare.15117102.v2
    From: man/greencrabData.Rd
* 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 serialization versions ... OK
* checking whether package ‘eDNAjoint’ can be installed ... [480s/480s] OK
* used C++ compiler: ‘Debian clang version 16.0.6 (11)’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking package directory ... OK
* checking for future file timestamps ... 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [8s/8s] OK
* checking Rd files ... [0s/0s] 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 ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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 ... [0m/30m] ERROR
Running examples in ‘eDNAjoint-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: traditionalModel
> ### Title: Specify and fit model using count data from traditional
> ###   (non-eDNA) surveys
> ### Aliases: traditionalModel
> 
> ### ** Examples
> 
> data(greencrabData)
> 
> # Examine data in list
> # This function uses only traditional survey count data and optionally the count type data
> names(greencrabData)
[1] "qPCR.N"     "qPCR.K"     "count"      "count.type"
> 
> # Note that the surveyed sites (rows) should match in the data
> dim(greencrabData$count)[1]
[1] 20
> dim(greencrabData$count.type)[1]
[1] 20
> 
> # Fit a model without estimating a catchability coefficient for traditional survey gear types.
> # This model assumes all traditional survey methods have the same catchability.
> # Count data is modeled using a poisson distribution.
> fit.no.q = traditionalModel(data=greencrabData, family='poisson', q=FALSE)

SAMPLING FOR MODEL 'traditional_pois' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 7.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.74 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:    1 / 3000 [  0%]  (Warmup)
Chain 1: Iteration:  300 / 3000 [ 10%]  (Warmup)
Chain 1: Iteration:  501 / 3000 [ 16%]  (Sampling)
Chain 1: Iteration:  800 / 3000 [ 26%]  (Sampling)
Chain 1: Iteration: 1100 / 3000 [ 36%]  (Sampling)
Chain 1: Iteration: 1400 / 3000 [ 46%]  (Sampling)
Chain 1: Iteration: 1700 / 3000 [ 56%]  (Sampling)
Chain 1: Iteration: 2000 / 3000 [ 66%]  (Sampling)
Chain 1: Iteration: 2300 / 3000 [ 76%]  (Sampling)
Chain 1: Iteration: 2600 / 3000 [ 86%]  (Sampling)
Chain 1: Iteration: 2900 / 3000 [ 96%]  (Sampling)
Chain 1: Iteration: 3000 / 3000 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.617 seconds (Warm-up)
Chain 1:                1.692 seconds (Sampling)
Chain 1:                2.309 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'traditional_pois' NOW (CHAIN 2).
Chain 2: 
Chain 2: Gradient evaluation took 7.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.71 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2: 
Chain 2: 
Chain 2: Iteration:    1 / 3000 [  0%]  (Warmup)
Chain 2: Iteration:  300 / 3000 [ 10%]  (Warmup)
Chain 2: Iteration:  501 / 3000 [ 16%]  (Sampling)
Chain 2: Iteration:  800 / 3000 [ 26%]  (Sampling)
Chain 2: Iteration: 1100 / 3000 [ 36%]  (Sampling)
Chain 2: Iteration: 1400 / 3000 [ 46%]  (Sampling)
Chain 2: Iteration: 1700 / 3000 [ 56%]  (Sampling)
Chain 2: Iteration: 2000 / 3000 [ 66%]  (Sampling)
Chain 2: Iteration: 2300 / 3000 [ 76%]  (Sampling)
Chain 2: Iteration: 2600 / 3000 [ 86%]  (Sampling)
Chain 2: Iteration: 2900 / 3000 [ 96%]  (Sampling)
Chain 2: Iteration: 3000 / 3000 [100%]  (Sampling)
Chain 2: 
Chain 2:  Elapsed Time: 0.665 seconds (Warm-up)
Chain 2:                1.848 seconds (Sampling)
Chain 2:                2.513 seconds (Total)
Chain 2: 

SAMPLING FOR MODEL 'traditional_pois' NOW (CHAIN 3).
Chain 3: 
Chain 3: Gradient evaluation took 6.9e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.69 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3: 
Chain 3: 
Chain 3: Iteration:    1 / 3000 [  0%]  (Warmup)
Chain 3: Iteration:  300 / 3000 [ 10%]  (Warmup)
Chain 3: Iteration:  501 / 3000 [ 16%]  (Sampling)
Chain 3: Iteration:  800 / 3000 [ 26%]  (Sampling)
Chain 3: Iteration: 1100 / 3000 [ 36%]  (Sampling)
Chain 3: Iteration: 1400 / 3000 [ 46%]  (Sampling)
Chain 3: Iteration: 1700 / 3000 [ 56%]  (Sampling)
Chain 3: Iteration: 2000 / 3000 [ 66%]  (Sampling)
Chain 3: Iteration: 2300 / 3000 [ 76%]  (Sampling)
Chain 3: Iteration: 2600 / 3000 [ 86%]  (Sampling)
Chain 3: Iteration: 2900 / 3000 [ 96%]  (Sampling)
Chain 3: Iteration: 3000 / 3000 [100%]  (Sampling)
Chain 3: 
Chain 3:  Elapsed Time: 0.616 seconds (Warm-up)
Chain 3:                1.418 seconds (Sampling)
Chain 3:                2.034 seconds (Total)
Chain 3: 

SAMPLING FOR MODEL 'traditional_pois' NOW (CHAIN 4).
Chain 4: 
Chain 4: Gradient evaluation took 6.9e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.69 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4: 
Chain 4: 
Chain 4: Iteration:    1 / 3000 [  0%]  (Warmup)
Chain 4: Iteration:  300 / 3000 [ 10%]  (Warmup)
Chain 4: Iteration:  501 / 3000 [ 16%]  (Sampling)
Chain 4: Iteration:  800 / 3000 [ 26%]  (Sampling)
Chain 4: Iteration: 1100 / 3000 [ 36%]  (Sampling)
Chain 4: Iteration: 1400 / 3000 [ 46%]  (Sampling)
Chain 4: Iteration: 1700 / 3000 [ 56%]  (Sampling)
Chain 4: Iteration: 2000 / 3000 [ 66%]  (Sampling)
Chain 4: Iteration: 2300 / 3000 [ 76%]  (Sampling)
Chain 4: Iteration: 2600 / 3000 [ 86%]  (Sampling)
Chain 4: Iteration: 2900 / 3000 [ 96%]  (Sampling)
Chain 4: Iteration: 3000 / 3000 [100%]  (Sampling)
Chain 4: 
Chain 4:  Elapsed Time: 0.651 seconds (Warm-up)
Chain 4:                1.629 seconds (Sampling)
Chain 4:                2.28 seconds (Total)
Chain 4: 
> 
> 
> # Fit a model estimating a catchability coefficient for traditional survey gear types.
> # This model does not assume all traditional survey methods have the same catchability.
> # Gear type 1 is used as the reference gear type.
> # The catchability of all other gear types are scaled relative to the catchability of type 1.
> # Count data is modeled using a negative binomial distribution.
> fit.q = traditionalModel(data=greencrabData, family='negbin', q=TRUE, q_ref=1)

SAMPLING FOR MODEL 'traditional_catchability_negbin' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 0.000253 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.53 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:    1 / 3000 [  0%]  (Warmup)
Chain 1: Iteration:  300 / 3000 [ 10%]  (Warmup)
Chain 1: Iteration:  501 / 3000 [ 16%]  (Sampling)
Chain 1: Iteration:  800 / 3000 [ 26%]  (Sampling)
Chain 1: Iteration: 1100 / 3000 [ 36%]  (Sampling)
Chain 1: Iteration: 1400 / 3000 [ 46%]  (Sampling)
Chain 1: Iteration: 1700 / 3000 [ 56%]  (Sampling)
Chain 1: Iteration: 2000 / 3000 [ 66%]  (Sampling)
Chain 1: Iteration: 2300 / 3000 [ 76%]  (Sampling)
Chain 1: Iteration: 2600 / 3000 [ 86%]  (Sampling)
Chain 1: Iteration: 2900 / 3000 [ 96%]  (Sampling)
Chain 1: Iteration: 3000 / 3000 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 2.707 seconds (Warm-up)
Chain 1:                6.736 seconds (Sampling)
Chain 1:                9.443 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'traditional_catchability_negbin' NOW (CHAIN 2).
Chain 2: 
Chain 2: Gradient evaluation took 0.000263 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.63 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2: 
Chain 2: 
Chain 2: Iteration:    1 / 3000 [  0%]  (Warmup)
Chain 2: Iteration:  300 / 3000 [ 10%]  (Warmup)
Chain 2: Iteration:  501 / 3000 [ 16%]  (Sampling)
Chain 2: Iteration:  800 / 3000 [ 26%]  (Sampling)
Chain 2: Iteration: 1100 / 3000 [ 36%]  (Sampling)
Chain 2: Iteration: 1400 / 3000 [ 46%]  (Sampling)
Chain 2: Iteration: 1700 / 3000 [ 56%]  (Sampling)
Chain 2: Iteration: 2000 / 3000 [ 66%]  (Sampling)
Chain 2: Iteration: 2300 / 3000 [ 76%]  (Sampling)
Chain 2: Iteration: 2600 / 3000 [ 86%]  (Sampling)
Chain 2: Iteration: 2900 / 3000 [ 96%]  (Sampling)
Chain 2: Iteration: 3000 / 3000 [100%]  (Sampling)
Chain 2: 
Chain 2:  Elapsed Time: 2.657 seconds (Warm-up)
Chain 2:                6.677 seconds (Sampling)
Chain 2:                9.334 seconds (Total)
Chain 2: 

SAMPLING FOR MODEL 'traditional_catchability_negbin' NOW (CHAIN 3).
Chain 3: 
Chain 3: Gradient evaluation took 0.000257 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 2.57 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3: 
Chain 3: 
Chain 3: Iteration:    1 / 3000 [  0%]  (Warmup)
Chain 3: Iteration:  300 / 3000 [ 10%]  (Warmup)
Chain 3: Iteration:  501 / 3000 [ 16%]  (Sampling)
Chain 3: Iteration:  800 / 3000 [ 26%]  (Sampling)
Chain 3: Iteration: 1100 / 3000 [ 36%]  (Sampling)
Chain 3: Iteration: 1400 / 3000 [ 46%]  (Sampling)
Chain 3: Iteration: 1700 / 3000 [ 56%]  (Sampling)
Chain 3: Iteration: 2000 / 3000 [ 66%]  (Sampling)
Chain 3: Iteration: 2300 / 3000 [ 76%]  (Sampling)
Chain 3: Iteration: 2600 / 3000 [ 86%]  (Sampling)
Chain 3: Iteration: 2900 / 3000 [ 96%]  (Sampling)
Chain 3: Iteration: 3000 / 3000 [100%]  (Sampling)
Chain 3: 
Chain 3:  Elapsed Time: 2.637 seconds (Warm-up)
Chain 3:                5.485 seconds (Sampling)
Chain 3:                8.122 seconds (Total)
Chain 3: 

SAMPLING FOR MODEL 'traditional_catchability_negbin' NOW (CHAIN 4).
Chain 4: 
Chain 4: Gradient evaluation took 0.000287 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 2.87 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4: 
Chain 4: 
Chain 4: Iteration:    1 / 3000 [  0%]  (Warmup)
Chain 4: Iteration:  300 / 3000 [ 10%]  (Warmup)
Chain 4: Iteration:  501 / 3000 [ 16%]  (Sampling)
Chain 4: Iteration:  800 / 3000 [ 26%]  (Sampling)
Chain 4: Iteration: 1100 / 3000 [ 36%]  (Sampling)
Chain 4: Iteration: 1400 / 3000 [ 46%]  (Sampling)
Chain 4: Iteration: 1700 / 3000 [ 56%]  (Sampling)
Chain 4: Iteration: 2000 / 3000 [ 66%]  (Sampling)
Chain 4: Iteration: 2300 / 3000 [ 76%]  (Sampling)
Chain 4: Iteration: 2600 / 3000 [ 86%]  (Sampling)
Chain 4: Iteration: 2900 / 3000 [ 96%]  (Sampling)
Chain 4: Iteration: 3000 / 3000 [100%]  (Sampling)
Chain 4: 
Chain 4:  Elapsed Time: 2.717 seconds (Warm-up)
Chain 4:                5.261 seconds (Sampling)
Chain 4:                7.978 seconds (Total)
Chain 4: 
> 
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("traditionalModel", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  576.046 4.404 580.576 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
Assertion failure at kmp_runtime.cpp(6918): temp_reg_status_file_name.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6918).
OMP: Hint Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see https://bugs.llvm.org/.
Assertion failure at kmp_runtime.cpp(6918): temp_reg_status_file_name.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6918).
OMP: Hint Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see https://bugs.llvm.org/.
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [296s/296s] OK
* checking PDF version of manual ... [3s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE