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Memory and compiler issues in version 0.6.0.0 (CRAN) #71

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gvegayon opened this issue Jan 17, 2025 · 1 comment · Fixed by #75
Closed

Memory and compiler issues in version 0.6.0.0 (CRAN) #71

gvegayon opened this issue Jan 17, 2025 · 1 comment · Fixed by #75
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@apulsipher

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@gvegayon
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We need to address some issues reported in CRAN with the last submission (adding the picture b/c it may be deleted):

Image

From the build vignettes log (related to lfmcmc):

--- re-building ‘getting-started.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR.Rcheck/vign_test/epiworldR/vignettes/getting-started_files/figure-html/unnamed-chunk-2-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 34276 bytes
Input file size = 34402 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 26910
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 26910

Output IDAT size = 26910 bytes (7366 bytes decrease)
Output file size = 26988 bytes (7414 bytes = 21.55% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR.Rcheck/vign_test/epiworldR/vignettes/getting-started_files/figure-html/unnamed-chunk-3-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 14330 bytes
Input file size = 15200 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 13126
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 12963
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 12963

Output IDAT size = 12963 bytes (1367 bytes decrease)
Output file size = 13041 bytes (2159 bytes = 14.20% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR.Rcheck/vign_test/epiworldR/vignettes/getting-started_files/figure-html/unnamed-chunk-4-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 44715 bytes
Input file size = 44853 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 35329
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 35329

Output IDAT size = 35329 bytes (9386 bytes decrease)
Output file size = 35407 bytes (9446 bytes = 21.06% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR.Rcheck/vign_test/epiworldR/vignettes/getting-started_files/figure-html/unnamed-chunk-6-1.png
672x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 78020 bytes
Input file size = 78206 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 62206
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 62206

Output IDAT size = 62206 bytes (15814 bytes decrease)
Output file size = 62284 bytes (15922 bytes = 20.36% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR.Rcheck/vign_test/epiworldR/vignettes/getting-started_files/figure-html/curves-including-vaccine-1.png
672x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 83085 bytes
Input file size = 83283 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 68984
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 68984

Output IDAT size = 68984 bytes (14101 bytes decrease)
Output file size = 69062 bytes (14221 bytes = 17.08% decrease)

--- finished re-building ‘getting-started.Rmd’

--- re-building ‘implementation.Rmd’ using rmarkdown
--- finished re-building ‘implementation.Rmd’

--- re-building ‘likelihood-free-mcmc.Rmd’ using rmarkdown
../inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp:164:25: runtime error: -inf is outside the range of representable values of type 'int'
    #0 0x7f01603cf981 in epiworld::LFMCMC<std::__1::vector<double, std::__1::allocator<double> > >::print(unsigned long) const /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR/src/../inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp:164:25
    #1 0x7f01603c2467 in print_lfmcmc_cpp(SEXPREC*, int) /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR/src/lfmcmc.cpp:429:17
    #2 0x7f0160322797 in _epiworldR_print_lfmcmc_cpp /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR/src/cpp11.cpp:621:27
    #3 0x556afc86ffa3 in R_doDotCall (/data/gannet/ripley/R/R-clang/bin/exec/R+0xf1fa3)
    #4 0x556afc8af0a5 in bcEval_loop eval.c
    #5 0x556afc8a774b in bcEval eval.c
    #6 0x556afc8a6ed4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x128ed4)
    #7 0x556afc8bf9f1 in R_execClosure eval.c
    #8 0x556afc8beedb in applyClosure_core eval.c
    #9 0x556afc8a80d5 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0x12a0d5)
    #10 0x556afc90bae5 in dispatchMethod objects.c
    #11 0x556afc90b578 in Rf_usemethod (/data/gannet/ripley/R/R-clang/bin/exec/R+0x18d578)
    #12 0x556afc90bf9d in do_usemethod (/data/gannet/ripley/R/R-clang/bin/exec/R+0x18df9d)
    #13 0x556afc8b0d0a in bcEval_loop eval.c
    #14 0x556afc8a774b in bcEval eval.c
    #15 0x556afc8a6ed4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x128ed4)
    #16 0x556afc8bf9f1 in R_execClosure eval.c
    #17 0x556afc8beedb in applyClosure_core eval.c
    #18 0x556afc8a7325 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x129325)
    #19 0x556afc8c635f in do_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x14835f)
    #20 0x556afc8ae012 in bcEval_loop eval.c
    #21 0x556afc8a774b in bcEval eval.c
    #22 0x556afc8a6ed4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x128ed4)
    #23 0x556afc8a79c3 in forcePromise eval.c
    #24 0x556afc8a6f9d in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x128f9d)
    #25 0x556afc8c6836 in do_withVisible (/data/gannet/ripley/R/R-clang/bin/exec/R+0x148836)
    #26 0x556afc9098f7 in do_internal (/data/gannet/ripley/R/R-clang/bin/exec/R+0x18b8f7)
    #27 0x556afc8b0d0a in bcEval_loop eval.c
    #28 0x556afc8a774b in bcEval eval.c
    #29 0x556afc8a6ed4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x128ed4)
    #30 0x556afc8a79c3 in forcePromise eval.c
    #31 0x556afc8a6f9d in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x128f9d)
    #32 0x556afc8a79c3 in forcePromise eval.c
    #33 0x556afc8bc1ab in getvar eval.c
    #34 0x556afc8b3f51 in bcEval_loop eval.c
    #35 0x556afc8a774b in bcEval eval.c
    #36 0x556afc8a6ed4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x128ed4)
    #37 0x556afc8bf9f1 in R_execClosure eval.c
    #38 0x556afc8beedb in applyClosure_core eval.c
    #39 0x556afc8a7325 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x129325)
    #40 0x556afc8c635f in do_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x14835f)
    #41 0x556afc8ae012 in bcEval_loop eval.c
    #42 0x556afc8a774b in bcEval eval.c
    #43 0x556afc8a6ed4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x128ed4)
    #44 0x556afc8bf9f1 in R_execClosure eval.c
    #45 0x556afc8beedb in applyClosure_core eval.c
    #46 0x556afc8a7325 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x129325)
    #47 0x556afc8bf9f1 in R_execClosure eval.c
    #48 0x556afc8beedb in applyClosure_core eval.c
    #49 0x556afc8b6185 in bcEval_loop eval.c
    #50 0x556afc8a774b in bcEval eval.c
    #51 0x556afc8a6ed4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x128ed4)
    #52 0x556afc8bf9f1 in R_execClosure eval.c
    #53 0x556afc8beedb in applyClosure_core eval.c
    #54 0x556afc8a7325 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0x129325)
    #55 0x556afc8f4e50 in Rf_ReplIteration (/data/gannet/ripley/R/R-clang/bin/exec/R+0x176e50)
    #56 0x556afc8f67ee in run_Rmainloop (/data/gannet/ripley/R/R-clang/bin/exec/R+0x1787ee)
    #57 0x556afc8f685a in Rf_mainloop (/data/gannet/ripley/R/R-clang/bin/exec/R+0x17885a)
    #58 0x556afc7e5a27 in main (/data/gannet/ripley/R/R-clang/bin/exec/R+0x67a27)
    #59 0x7f017282950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #60 0x7f01728295c8 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #61 0x556afc7e5944 in _start (/data/gannet/ripley/R/R-clang/bin/exec/R+0x67944)

SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior ../inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp:164:25 
** Processing: /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR.Rcheck/vign_test/epiworldR/vignettes/likelihood-free-mcmc_files/figure-html/post-dist-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 36701 bytes
Input file size = 36827 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 32525
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 32525

Output IDAT size = 32525 bytes (4176 bytes decrease)
Output file size = 32603 bytes (4224 bytes = 11.47% decrease)

--- finished re-building ‘likelihood-free-mcmc.Rmd’

--- re-building ‘mixing.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR.Rcheck/vign_test/epiworldR/vignettes/mixing_files/figure-html/model-simulate-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76386 bytes
Input file size = 76572 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 58365
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 58365

Output IDAT size = 58365 bytes (18021 bytes decrease)
Output file size = 58443 bytes (18129 bytes = 23.68% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR.Rcheck/vign_test/epiworldR/vignettes/mixing_files/figure-html/transmissions-plot-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37991 bytes
Input file size = 38117 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 34960
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 34960

Output IDAT size = 34960 bytes (3031 bytes decrease)
Output file size = 35038 bytes (3079 bytes = 8.08% decrease)

--- finished re-building ‘mixing.Rmd’

--- re-building ‘run-multiple.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR.Rcheck/vign_test/epiworldR/vignettes/run-multiple_files/figure-html/plotting seirconn epicurves-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 23027 bytes
Input file size = 23909 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 21601
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 21601

Output IDAT size = 21601 bytes (1426 bytes decrease)
Output file size = 21679 bytes (2230 bytes = 9.33% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang-UBSAN/epiworldR.Rcheck/vign_test/epiworldR/vignettes/run-multiple_files/figure-html/reproductive number plot-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21670 bytes
Input file size = 22552 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20021
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20021

Output IDAT size = 20021 bytes (1649 bytes decrease)
Output file size = 20099 bytes (2453 bytes = 10.88% decrease)

--- finished re-building ‘run-multiple.Rmd’
@gvegayon gvegayon marked this as a duplicate of EpiForeSITE/software#37 Jan 17, 2025
@apulsipher apulsipher self-assigned this Jan 23, 2025
This was referenced Jan 23, 2025
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apulsipher commented Jan 23, 2025 •
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@gvegayon I think I've resolved the runtime error in UofUEpiBio/epiworld#50 (requested your review), but do I also need to handle the

Input IDAT size = 21670 bytes
Input file size = 22552 bytes

Bits? If so, I don't understand what problem is with these sections.

@apulsipher apulsipher linked a pull request Jan 28, 2025 that will close this issue
Fix clang compiler bug for CRAN submission #75
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Fix clang compiler bug for CRAN submission UofUEpiBio/epiworldR
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@gvegayon @apulsipher