* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘mizer’ ...
** this is package ‘mizer’ version ‘3.4.0’
** package ‘mizer’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-16 (Debian 16.2.0-1) 16.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpqimHRY/R.INSTALL26cf66ba005af/mizer/src'
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c inner_project_loop.cpp -o inner_project_loop.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c project_n_loop.cpp -o project_n_loop.o
g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o mizer.so RcppExports.o inner_project_loop.o project_n_loop.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpqimHRY/R.INSTALL26cf66ba005af/mizer/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpqimHRY/R.INSTALL26cf66ba005af/mizer/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpqimHRY/R.INSTALL26cf66ba005af/mizer/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-mizer/00new/mizer/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘mizer’
finding HTML links ... done
ArrayResourceBySize html
ArrayResourceBySize_plot_data html
ArraySpeciesBySize html
ArraySpeciesBySize_plot_data html
ArrayTimeByResourceBySize html
ArrayTimeBySpecies html
ArrayTimeBySpeciesBySize html
BevertonHoltRDD html
MizerParams-class html
MizerParams html
MizerScan html
MizerSim-class html
MizerSim html
N html
NOther html
NS_interaction html
NS_params html
NS_sim html
NS_species_params html
NS_species_params_gears html
RickerRDD html
SheperdRDD html
addPlot html
addSpecies html
add_scan_annotations html
add_total_line html
adjustSizeGrid html
age_mat html
age_mat_vB html
animate html
append_total_line html
apply_wlim html
array_density_wrt html
array_log_y html
array_type html
array_types html
array_ylim html
as.data.frame html
as_series_matrix html
bin_average_weight html
bin_midpoints html
box_pred_kernel html
broadcast_dims html
calc_selectivity html
calibrateBiomass html
calibrateNumber html
calibrate_to html
cdf_y_label html
check_band_vars html
check_finite html
check_per_log_size html
coerceToExtensionClass html
collect_dimnames html
compareParams html
completeSpeciesParams html
constantEggRDI html
constantRDD html
constant_other html
convert_density_units html
convert_plot_density_axis html
convert_plot_size_axis html
convert_plot_spectrum_axis html
copy_scan_attributes html
customFunction html
cutoff_min_w html
default_info_level html
default_pred_kernel_params html
defaults_edition html
density_measure_jacobian html
density_measure_weight html
density_measures html
density_size_unit html
density_target_measure html
different html
dim_extents html
dim_from_labels html
distanceMaxRelRDI html
distanceSSLogN html
dot-checkRateFunctionOutput html
dot-hasSlot html
double_sigmoid_length html
emptyParams html
encounter_kernel html
ensureExtensionNamespaces html
expandSizeGrid html
expand_kernel_offsets html
extensionRequirements html
extensionVersion html
extensionVersions html
extension_needs_upgrading html
filter_plot_length_limits html
finalN html
findSteadyState html
flux_from_rates html
flux_units html
free_gear_name html
frozen_rate_params html
gaussian_mixture_pred_kernel html
gear_names html
gear_params html
getBiomass html
getCommunitySlope html
getCriticalFeedingLevel html
getDiet html
getDiffusion html
getDiscreteStability html
getEGrowth html
getERepro html
getEReproAndGrowth html
getESpawning html
getEffort html
getEncounter html
getFMort html
getFMortGear html
getFeedingLevel html
getFlux html
getFluxGradient html
getGrowthCurves html
getM2 html
getM2Background html
getMeanMaxWeight html
getMeanWeight html
getMort html
getN html
getOscillationModeSim html
getParams html
getPhiPrey html
getPredMort html
getPredRate html
getProportionOfLargeFish html
getRDD html
getRDI html
getRates html
getRequiredRDD html
getResourceMort html
getSSB html
getSimParams html
getStability html
getSteadyResidual html
getTimes html
getTrophicLevel html
getTrophicLevelBySpecies html
getYield html
getYieldGear html
getZ html
get_ArrayResourceBySize_w html
get_ArraySpeciesBySize_w html
get_ArrayTimeBySpeciesBySize_w html
get_f0_default html
get_gamma_default html
get_h_default html
get_initial_n html
get_ks_default html
get_phi html
get_sim_rate_slice html
get_sim_rate_time_elements html
get_size_range_array html
get_species_size_rate_from_sim html
get_species_time_rate_from_sim html
get_steady_state_n html
get_time_elements html
get_yield_observed html
indicator_functions html
initialN-set html
initialNOther-set html
initialNResource-set html
initial_effort html
install_tmp_gear html
inter html
interpolate_in_log_size html
interpolate_relative_frames html
isSteady html
isVersionRequirement html
is_validated html
knife_edge html
knife_edge_length html
l2w html
length_at_size html
log_breaks html
lognormal_pred_kernel html
makeExtensions html
make_linesize html
make_mizer_plot html
markBackground html
matchBiomasses html
matchGrowth html
matchNumbers html
match_to html
measure_on_attractor html
merge_dim_labels html
mizer-package html
mizerDiffusion html
mizerEGrowth html
mizerERepro html
mizerEReproAndGrowth html
mizerEncounter html
mizerFMort html
mizerFMortGear html
mizerFeedingLevel html
mizerMort html
mizerPredMort html
mizerPredRate html
mizerRDI html
mizerRates html
mizerResourceMort html
mizer_needs_upgrading html
mizer_rates_subset html
mizer_tooltip_vars html
model_observation html
needed_rates html
needs_upgrading html
newCommunityParams html
newMultispeciesParams html
newSingleSpeciesParams html
newTraitParams html
noRDD html
objectExtensions html
observation_columns html
other_mort html
params_as_sim html
parsePlotLog html
plot.ArrayResourceBySize html
plot.ArraySpeciesBySize html
plot.ArrayTimeByResourceBySize html
plot.ArrayTimeBySpecies html
plot.ArrayTimeBySpeciesBySize html
plot.MizerScan html
plot html
plot2 html
plotBiomass html
plotBiomassObservedVsModel html
plotCDF html
plotCDF2 html
plotComparisonDataFrame html
plotDataFrame html
plotDiet html
plotFMort html
plotFeedingLevel html
plotGrowthCurves html
plotHover html
plotM2 html
plotMizerParams html
plotMizerSim html
plotPredMort html
plotRelative html
plotRelativeDataFrame html
plotSpectra html
plotSpectra2 html
plotSpectraRelative html
plotYield html
plotYieldGear html
plotYieldObservedVsModel html
plotYieldVsF html
plot_cdf html
plot_diet html
plot_feeding_level html
plot_growth_curves html
plot_length_params html
plot_size_axis html
plot_size_tooltip html
plot_size_x_var html
plot_size_xlab html
plot_size_xlim html
plot_spectra html
plot_y_is_log html
plotting_functions html
power_law_bin_average html
power_law_pred_kernel html
prepare_ArrayTimeBySpecies_plot_data html
prepare_MizerScan_plot_data html
prepare_spectra_cdf_data html
print html
print.mizer_plot html
project html
projectRDD html
projectUntilSettled html
project_n html
project_n_2 html
project_n_tr_bdf2 html
project_simple html
proportion_ylim html
reconcileSpeciesParams html
recordExtension html
record_given_species_params html
reexports html
relative_difference html
removeBackgroundSpecies html
removeSpecies html
renameGear html
renameSpecies html
repair_params html
report_scan_convergence html
resolve_array_type html
resolve_cdf_power html
resolve_second_order_w html
resolve_spectrum_power html
resource_constant html
resource_length_defaults html
resource_length_params html
resource_logistic html
resource_params html
resource_power_law html
resource_semichemostat html
runExtensionUpgrades html
saveParams html
scaleModel html
scaleRates html
scanEffort html
scanModel html
scan_gear_installed html
scan_plot_params html
scan_x_var html
scan_y_label html
second_order_w html
select_gear_rows html
select_scan_series html
setBevertonHolt html
setColours html
setComponent html
setExtDiffusion html
setExtEncounter html
setExtMort html
setFishing html
setInitialValues html
setInteraction html
setMaxIntakeRate html
setMetabolicRate html
setMetadata html
setParams html
setPredKernel html
setRateFunction html
setReproduction html
setResource html
setRmax html
setSearchVolume html
set_community_model html
set_multispecies_model html
set_scan_maximum html
set_species_param_default html
set_trait_model html
sigmoid_length html
sigmoid_weight html
signal_defaulted_length_weight html
signal_frozen html
signal_frozen_changes html
signal_gear_params_changes html
signal_ignored_changes html
signal_info html
signal_not_recalculated html
signal_removed_species_params html
simExtensionClass html
sim_size_rate html
sim_species_rate html
sizeIntegral html
size_dim_labels html
slot-set html
slot html
slotNames html
species_params html
species_size_range_mask html
spectra_bin_width html
spectra_y_label html
spectrum_density_wrt html
steadySingleSpecies html
str html
summary html
summary_functions html
superseded_accessors html
superseded_steady html
sweep_arms html
total_contributors html
trapezoidal_bin_average html
truncated_lognormal_pred_kernel html
tuneSteadyState html
upgrade.MizerParams html
upgrade.MizerSim html
upgradeParams html
upgradeSim html
upgrade_s4_to_s3 html
use_predation_diffusion html
validEffortVector html
validGearParams html
validObject html
validParams html
validSim html
validSpeciesParams html
valid_gears_arg html
valid_species_arg html
validateExtensionsVector html
validate_array_type html
validate_density_wrt html
validate_second_order_w html
validation_key html
w html
with_info_level html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mizer)