Error(s) in re-building vignettes:
--- re-building ‘rodeoVignette.Rmd’ using rmarkdown
make[1]: Entering directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
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gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/vignetteData/fortran/functionsCode.f95 -o /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/vignetteData/fortran/functionsCode.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61725f3534fa.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61725f3534fa.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61725f3534fa.f95:65:39:

   65 |   double precision, dimension(NVAR*NBOX), intent(in):: var
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61725f3534fa.f95:66:39:

   66 |   double precision, dimension(NPAR*NBOX), intent(in):: par
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61725f3534fa.f95:59:20:

   59 | subroutine drvs(time, var, par, NBOX, dydt, pro)
      |                    1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617261371b.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617261371b.o
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo6172369632e.so /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/vignetteData/fortran/functionsCode.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61725f3534fa.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617261371b.o -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
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make[1]: Entering directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61721b8b6568.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61721b8b6568.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61721b8b6568.f95:83:39:

   83 |   double precision, dimension(NVAR*NBOX), intent(in):: var
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61721b8b6568.f95:84:39:

   84 |   double precision, dimension(NPAR*NBOX), intent(in):: par
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61721b8b6568.f95:77:20:

   77 | subroutine drvs(time, var, par, NBOX, dydt, pro)
      |                    1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61728760059.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61728760059.o
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61725f6de70b.so /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61721b8b6568.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61728760059.o -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Entering directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
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make[1]: Entering directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61726fd138f.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61726fd138f.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61726fd138f.f95:59:39:

   59 |   double precision, dimension(NVAR*NBOX), intent(in):: var
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61726fd138f.f95:60:39:

   60 |   double precision, dimension(NPAR*NBOX), intent(in):: par
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61726fd138f.f95:53:20:

   53 | subroutine drvs(time, var, par, NBOX, dydt, pro)
      |                    1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617210eeca60.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617210eeca60.o
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo6172201257f5.so /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61726fd138f.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617210eeca60.o -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Entering directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
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make[1]: Entering directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/advectionDispersion/functions.f95 -o /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/advectionDispersion/functions.o
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/advectionDispersion/functions.f95:14:20:

   14 |   function cDn (time) result (r)
      |                    1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/advectionDispersion/functions.f95:8:20:

    8 |   function cUp (time) result (r)
      |                    1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617245cd9743.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617245cd9743.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617245cd9743.f95:64:39:

   64 |   double precision, dimension(NVAR*NBOX), intent(in):: var
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617245cd9743.f95:65:39:

   65 |   double precision, dimension(NPAR*NBOX), intent(in):: par
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617279460c3e.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617279460c3e.o
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617229f24b30.so /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/advectionDispersion/functions.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617245cd9743.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617279460c3e.o -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
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gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/groundwater/functions.f95 -o /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/groundwater/functions.o
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/groundwater/functions.f95:23:38:

   23 |   double precision function hRiv (time)
      |                                      1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/groundwater/functions.f95:18:37:

   18 |   double precision function rch (time)
      |                                     1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61721c63040f.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61721c63040f.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61721c63040f.f95:70:39:

   70 |   double precision, dimension(NVAR*NBOX), intent(in):: var
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61721c63040f.f95:71:39:

   71 |   double precision, dimension(NPAR*NBOX), intent(in):: par
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61725e7f0c9.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61725e7f0c9.o
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61729157d9c.so /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/groundwater/functions.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61721c63040f.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61725e7f0c9.o -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
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gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/tetracycline/functions.f95 -o /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/tetracycline/functions.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617210f27d6a.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617210f27d6a.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617210f27d6a.f95:165:39:

  165 |   double precision, dimension(NVAR*NBOX), intent(in):: var
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617210f27d6a.f95:166:39:

  166 |   double precision, dimension(NPAR*NBOX), intent(in):: par
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617210f27d6a.f95:159:20:

  159 | subroutine drvs(time, var, par, NBOX, dydt, pro)
      |                    1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo6172725cf015.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo6172725cf015.o
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617228bc1406.so /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/1D/tetracycline/functions.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617210f27d6a.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo6172725cf015.o -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
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gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95 -o /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.o
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95:18:18:

   18 | function sInf(time) result (res)
      |                  1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95:12:18:

   12 | function xInf(time) result (res)
      |                  1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95:6:15:

    6 | function q(time) result (res)
      |               1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61726f10bb6.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61726f10bb6.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61726f10bb6.f95:80:39:

   80 |   double precision, dimension(NVAR*NBOX), intent(in):: var
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61726f10bb6.f95:81:39:

   81 |   double precision, dimension(NPAR*NBOX), intent(in):: par
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo6172715737c1.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo6172715737c1.o
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo617273810846.so /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo61726f10bb6.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rodeo6172715737c1.o -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
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gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file6172bbe4a96.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file6172bbe4a96.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file6172bbe4a96.f95:269:11:

  269 | integer:: i
      |           1
Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable]
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file6172bbe4a96.f95:301:0:

  301 |   if (abs(hnext) .lt. hmin) then
      | 
Warning: ‘hnext’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95 -o /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.o
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95:18:18:

   18 | function sInf(time) result (res)
      |                  1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95:12:18:

   12 | function xInf(time) result (res)
      |                  1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95:6:15:

    6 | function q(time) result (res)
      |               1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file61727b93f8f7.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file61727b93f8f7.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file61727b93f8f7.f95:67:39:

   67 |   double precision, dimension(NVAR*NBOX), intent(in):: var
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file61727b93f8f7.f95:68:39:

   68 |   double precision, dimension(NPAR*NBOX), intent(in):: par
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file617214c999ce.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file617214c999ce.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file617214c999ce.f95:18:43:

   18 |       double precision, dimension(NVAR*NBOX), intent(in):: var
      |                                           1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file617214c999ce.f95:19:43:

   19 |       double precision, dimension(NPAR*NBOX), intent(in):: par
      |                                           1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file617214c999ce.f95:30:46:

   30 |   subroutine derivs_wrapped(t,u,par,dudt,error)
      |                                              1
Warning: Dummy argument ‘error’ at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument]
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rk56172347a5e9c.so /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file6172bbe4a96.o /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file61727b93f8f7.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file617214c999ce.o -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Entering directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Entering directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Entering directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Entering directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file61729371e7f.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file61729371e7f.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file61729371e7f.f95:269:11:

  269 | integer:: i
      |           1
Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable]
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file61729371e7f.f95:301:0:

  301 |   if (abs(hnext) .lt. hmin) then
      | 
Warning: ‘hnext’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95 -o /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.o
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95:18:18:

   18 | function sInf(time) result (res)
      |                  1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95:12:18:

   12 | function xInf(time) result (res)
      |                  1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
/data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95:6:15:

    6 | function q(time) result (res)
      |               1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file617253a5c88e.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file617253a5c88e.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file617253a5c88e.f95:70:39:

   70 |   double precision, dimension(NVAR*NBOX), intent(in):: var
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file617253a5c88e.f95:71:39:

   71 |   double precision, dimension(NPAR*NBOX), intent(in):: par
      |                                       1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file617253a5c88e.f95:64:22:

   64 | subroutine derivs(time, var, par, NBOX, dydt, pro)
      |                      1
Warning: Unused dummy argument ‘time’ at (1) [-Wunused-dummy-argument]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c  /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file6172230409e6.f95 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file6172230409e6.o
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file6172230409e6.f95:18:43:

   18 |       double precision, dimension(NVAR*NBOX), intent(in):: var
      |                                           1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file6172230409e6.f95:19:43:

   19 |       double precision, dimension(NPAR*NBOX), intent(in):: par
      |                                           1
Warning: GNU Extension: Symbol ‘nbox’ is used before it is typed at (1)
/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file6172230409e6.f95:30:46:

   30 |   subroutine derivs_wrapped(t,u,par,dudt,error)
      |                                              1
Warning: Dummy argument ‘error’ at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument]
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/rk5617210205046.so /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file61729371e7f.o /data/gannet/ripley/R/packages/tests-clang/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file617253a5c88e.o /tmp/RtmpWKgtwV/working_dir/Rtmpjcph07/file6172230409e6.o -lgfortran -lm -lquadmath
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Entering directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Entering directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
make[1]: Leaving directory '/tmp/RtmpWKgtwV/working_dir/Rtmpjcph07'
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'rodeoVignette.Rmd' failed with diagnostics:
Failed to compile rodeoVignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See rodeoVignette.log for more info.
--- failed re-building ‘rodeoVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘rodeoVignette.Rmd’

Error: Vignette re-building failed.
Execution halted