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Intentional?

Hi,
I tried to test your igGeneUsage on my Windows pc, but get error below, please help me!!!
Thank you
Joan

M <- DGU(usage.data = IGHV_HCV, # input data

•      mcmc.warmup = 250, # how many MCMC warm-ups per chain (default: 500)
  

•      mcmc.steps = 1000, # how many MCMC steps per chain (default: 1,500)
  

•      mcmc.chains = 2, # how many MCMC chain to run (default: 4)
  

•      mcmc.cores = 1, # how many PC cores to use? (e.g. parallel chains)
  

•      hdi.level = 0.95, # highest density interval level (de fault: 0.95)
  

•      adapt.delta = 0.95, # MCMC target acceptance rate (default: 0.95)
  

•      max.treedepth = 10) # tree depth evaluated at each step (default: 12)
  

Compiling model ...

make cmd is
make -f "C:/PROGRA1/R/R-421.1/etc/x64/Makeconf" -f "C:/PROGRA1/R/R-421.1/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file6e843f2f6e5b.dll" WIN=64 TCLBIN= OBJECTS="file6e843f2f6e5b.o"

make would use
if test "zfile6e843f2f6e5b.o" != "z"; then
if test -e "file6e843f2f6e5b-win.def"; then
echo g++ -shared -s -static-libgcc -o file6e843f2f6e5b.dll file6e843f2f6e5b-win.def file6e843f2f6e5b.o -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA1/R/R-421.1/bin/x64" -lR ;
g++ -shared -s -static-libgcc -o file6e843f2f6e5b.dll file6e843f2f6e5b-win.def file6e843f2f6e5b.o -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA1/R/R-421.1/bin/x64" -lR ;
else
echo EXPORTS > tmp.def;
nm file6e843f2f6e5b.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def;
echo g++ -shared -s -static-libgcc -o file6e843f2f6e5b.dll tmp.def file6e843f2f6e5b.o -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA1/R/R-421.1/bin/x64" -lR ;
g++ -shared -s -static-libgcc -o file6e843f2f6e5b.dll tmp.def file6e843f2f6e5b.o -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA1/R/R-421.1/bin/x64" -lR ;
rm -f tmp.def;
fi
fi
Error in compileCode(f, code, language = language, verbose = verbose) :
C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file6e843f2f6e5b.o:file6e843f2f6e5b.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file6e843f2f6e5b.o:file6e843f2f6e5b.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file6e843f2f6e5b.o:file6e843f2f6e5b.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x3a): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file6e843f2f6e5b.o:file6e843f2f6e5b.cpp:(.text$_ZN3tbb10interface
In addition: Warning message:
In checkUsageData(usage.data = usage.data) :
no replicates provided for at least one of the conditions.
Error in sink(type = "output") : invalid connection

Paired vs. replicated setup check details

Hi -- the chunks in the vignette are all eval=F? This prevents the Bioconductor build system from
realistically checking the package. I tried running the vignette (changing eval=F to eval=TRUE,
and using IgGeneUsage:::DGU because DGU function is not exported) and after two chains finish
we have:

Computing summaries ... 

Posterior extraction ... 

Computing probability of DGU ... 

Computing posterior predictions ... 

Error: $ operator is invalid for atomic vectors
In addition: Warning messages:
1: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess 
2: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess 

Enter a frame number, or 0 to exit   

1: source("IgUsageCaseStudies.R", echo = TRUE)
2: withVisible(eval(ei, envir))
3: eval(ei, envir)
4: eval(ei, envir)
5: IgUsageCaseStudies.R#64: IgGeneUsage:::DGU(usage.data = IGHV_HCV, mcmc.warm
6: getPpcRepertoire(glm = glm, usage.data = usage.data, hdi.level = hdi.level)

> sessionInfo()
R version 4.2.0 RC (2022-04-15 r82209)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /home/stvjc/R-4-2-dist/lib/R/lib/libRblas.so
LAPACK: /home/stvjc/R-4-2-dist/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] reshape2_1.4.4              rstan_2.21.5               
 [3] ggrepel_0.9.1               gridExtra_2.3              
 [5] ggforce_0.3.3               ggplot2_3.3.6              
 [7] IgGeneUsage_1.11.1          StanHeaders_2.21.0-7       
 [9] SummarizedExperiment_1.26.1 Biobase_2.56.0             
[11] GenomicRanges_1.48.0        GenomeInfoDb_1.32.2        
[13] IRanges_2.30.0              S4Vectors_0.34.0           
[15] BiocGenerics_0.42.0         MatrixGenerics_1.8.0       
[17] matrixStats_0.62.0          Rcpp_1.0.8.3               
[19] knitr_1.39                  rmarkdown_2.14             

loaded via a namespace (and not attached):
 [1] lattice_0.20-45        prettyunits_1.1.1      ps_1.7.0              
 [4] assertthat_0.2.1       digest_0.6.29          utf8_1.2.2            
 [7] plyr_1.8.7             R6_2.5.1               evaluate_0.15         
[10] highr_0.9              pillar_1.7.0           zlibbioc_1.42.0       
[13] rlang_1.0.2            callr_3.7.0            Matrix_1.4-1          
[16] startup_0.18.0         labeling_0.4.2         stringr_1.4.0         
[19] loo_2.5.1              RCurl_1.98-1.6         polyclip_1.10-0       
[22] munsell_0.5.0          DelayedArray_0.22.0    compiler_4.2.0        
[25] xfun_0.31              pkgconfig_2.0.3        pkgbuild_1.3.1        
[28] htmltools_0.5.2        tidyselect_1.1.2       tibble_3.1.7          
[31] GenomeInfoDbData_1.2.8 codetools_0.2-18       fansi_1.0.3           
[34] crayon_1.5.1           dplyr_1.0.9            withr_2.5.0           
[37] MASS_7.3-57            bitops_1.0-7           grid_4.2.0            
[40] gtable_0.3.0           lifecycle_1.0.1        DBI_1.1.2             
[43] magrittr_2.0.3         scales_1.2.0           RcppParallel_5.1.5    
[46] cli_3.3.0              stringi_1.7.6          farver_2.1.0          
[49] XVector_0.36.0         ellipsis_0.3.2         generics_0.1.2        
[52] vctrs_0.4.1            tools_4.2.0            glue_1.6.2            
[55] tweenr_1.0.2           purrr_0.3.4            parallel_4.2.0        
[58] processx_3.6.0         fastmap_1.1.0          inline_0.3.19         
[61] colorspace_2.0-3  

Allow user to modify priors (big re-design will be needed)

While LOOIC analysis does not "recommend" that with the given datasets, this might be useful.

What to pay attention to:

• effects on runtime
• effects on convergence
• effect on small-sample analyses