Closed marosteg closed 3 years ago
Can you provide a MWE?
I assume you're working from the dev
branch? These functions have both been working fine for me lately so perhaps something inherent to your specific use case.
I am experiencing issues with the parallelized versions of the sst and ohc likelihood calculation functions. Notably,
calc.sst()
yields likelihoods whilecalc.sst.par
yields:Error in L.sst[, , i] <- lik.sst[[i]] : number of items to replace is not a multiple of replacement length
which stems from code unique to the parallelized function.
This issue stemmed from the use of MUR sst data which was being automatically aggregated (coarsened) to improve likelihood calculation speed. The aggregated sst data was not matched in dimensions by the attempted likelihood calculation, causing an error. This has been fixed with #43. Please review and/or confirm the fix and we'll merge to dev
.
Similarly,
calc.ohc
yields likelihoods whilecalc.ohc.par
does not (it does not yield an error though).
I am unable to reproduce this issue. I can calculate OHC based likelihoods using either approach. Here's the output of plot(L.ohc.par[[1:5]])
with your example data (note that days 4 and 5 are missing input pdt data):
I just get five blank days (rather than three with likelihoods and two blank). Perhaps compare sessions?
sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] HMMoce_1.1.0 analyzePSAT_0.1.0 raster_3.4-5 sp_1.4-4 reshape2_1.4.4
[6] tidyfast_0.2.1 tags2etuff_1.0.0 forcats_0.4.0 stringr_1.4.0 dplyr_1.0.2
[11] purrr_0.3.4 readr_1.3.1 tidyr_1.1.2 tibble_3.0.4 tidyverse_1.3.0
[16] ggplot2_3.3.2 lubridate_1.7.9.2 fields_11.6 spam_2.5-1 dotCall64_1.0-0
[21] pracma_2.2.9 Matrix_1.2-18 oce_1.2-0 gsw_1.0-5 testthat_2.3.2
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 ellipsis_0.3.1 rgdal_1.4-8 rprojroot_1.3-2 fs_1.3.1
[6] rstudioapi_0.11 farver_2.0.3 remotes_2.2.0 fansi_0.4.1 xml2_1.2.2
[11] codetools_0.2-16 ncdf4_1.17 doParallel_1.0.16 polyclip_1.10-0 pkgload_1.1.0
[16] readbitmap_0.1.5 jsonlite_1.7.1 broom_0.7.0 dbplyr_1.4.2 png_0.1-7
[21] rgeos_0.5-5 ggforce_0.3.2 compiler_3.6.3 httr_1.4.2 backports_1.1.8
[26] assertthat_0.2.1 bmp_0.3 cli_2.0.2 tweenr_1.0.1 prettyunits_1.1.1
[31] tools_3.6.3 igraph_1.2.5 gtable_0.3.0 glue_1.4.2 maps_3.3.0
[36] Rcpp_1.0.5 cellranger_1.1.0 RNetCDF_2.4-2 vctrs_0.3.2 iterators_1.0.12
[41] ps_1.3.4 rvest_0.3.6 lifecycle_0.2.0 devtools_2.3.2 MASS_7.3-53
[46] scales_1.1.1 hms_0.5.3 parallel_3.6.3 RColorBrewer_1.1-2 curl_4.3
[51] memoise_1.1.0 gridExtra_2.3 stringi_1.4.6 imager_0.42.3 maptools_1.0-2
[56] desc_1.2.0 foreach_1.5.1 tiff_0.1-5 pkgbuild_1.1.0 rlang_0.4.7
[61] pkgconfig_2.0.3 bitops_1.0-6 lattice_0.20-41 labeling_0.3 processx_3.4.4
[66] tidyselect_1.1.0 fasttime_1.0-2 plyr_1.8.6 magrittr_2.0.1 R6_2.4.1
[71] generics_0.0.2 DBI_1.1.0 pillar_1.4.6 haven_2.3.1 foreign_0.8-75
[76] withr_2.3.0 RCurl_1.98-1.2 modelr_0.1.5 crayon_1.3.4 utf8_1.1.4
[81] jpeg_0.1-8.1 usethis_1.6.3 locfit_1.5-9.4 readxl_1.3.1 data.table_1.12.8
[86] callr_3.5.1 reprex_0.3.0 digest_0.6.25 munsell_0.5.0 sessioninfo_1.1.1
I just get five blank days (rather than three with likelihoods and two blank). Perhaps compare sessions?
sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] HMMoce_1.1.0 analyzePSAT_0.1.0 raster_3.4-5 sp_1.4-4 reshape2_1.4.4 [6] tidyfast_0.2.1 tags2etuff_1.0.0 forcats_0.4.0 stringr_1.4.0 dplyr_1.0.2 [11] purrr_0.3.4 readr_1.3.1 tidyr_1.1.2 tibble_3.0.4 tidyverse_1.3.0 [16] ggplot2_3.3.2 lubridate_1.7.9.2 fields_11.6 spam_2.5-1 dotCall64_1.0-0 [21] pracma_2.2.9 Matrix_1.2-18 oce_1.2-0 gsw_1.0-5 testthat_2.3.2 loaded via a namespace (and not attached): [1] colorspace_1.4-1 ellipsis_0.3.1 rgdal_1.4-8 rprojroot_1.3-2 fs_1.3.1 [6] rstudioapi_0.11 farver_2.0.3 remotes_2.2.0 fansi_0.4.1 xml2_1.2.2 [11] codetools_0.2-16 ncdf4_1.17 doParallel_1.0.16 polyclip_1.10-0 pkgload_1.1.0 [16] readbitmap_0.1.5 jsonlite_1.7.1 broom_0.7.0 dbplyr_1.4.2 png_0.1-7 [21] rgeos_0.5-5 ggforce_0.3.2 compiler_3.6.3 httr_1.4.2 backports_1.1.8 [26] assertthat_0.2.1 bmp_0.3 cli_2.0.2 tweenr_1.0.1 prettyunits_1.1.1 [31] tools_3.6.3 igraph_1.2.5 gtable_0.3.0 glue_1.4.2 maps_3.3.0 [36] Rcpp_1.0.5 cellranger_1.1.0 RNetCDF_2.4-2 vctrs_0.3.2 iterators_1.0.12 [41] ps_1.3.4 rvest_0.3.6 lifecycle_0.2.0 devtools_2.3.2 MASS_7.3-53 [46] scales_1.1.1 hms_0.5.3 parallel_3.6.3 RColorBrewer_1.1-2 curl_4.3 [51] memoise_1.1.0 gridExtra_2.3 stringi_1.4.6 imager_0.42.3 maptools_1.0-2 [56] desc_1.2.0 foreach_1.5.1 tiff_0.1-5 pkgbuild_1.1.0 rlang_0.4.7 [61] pkgconfig_2.0.3 bitops_1.0-6 lattice_0.20-41 labeling_0.3 processx_3.4.4 [66] tidyselect_1.1.0 fasttime_1.0-2 plyr_1.8.6 magrittr_2.0.1 R6_2.4.1 [71] generics_0.0.2 DBI_1.1.0 pillar_1.4.6 haven_2.3.1 foreign_0.8-75 [76] withr_2.3.0 RCurl_1.98-1.2 modelr_0.1.5 crayon_1.3.4 utf8_1.1.4 [81] jpeg_0.1-8.1 usethis_1.6.3 locfit_1.5-9.4 readxl_1.3.1 data.table_1.12.8 [86] callr_3.5.1 reprex_0.3.0 digest_0.6.25 munsell_0.5.0 sessioninfo_1.1.1
This doesnt look out of the ordinary. Try using the calc.ohc.par()
function this recent push https://github.com/camrinbraun/HMMoce/commit/1a54e99e161cbe811615014961f27cabf6ff9250
@marosteg is this the lingering issue you mentioned to me? still having problems with this?
I don't seem to have issues on this front anymore. The lingering thing is for you to test and approve #52.
I am experiencing issues with the parallelized versions of the sst and ohc likelihood calculation functions. Notably,
calc.sst()
yields likelihoods whilecalc.sst.par
yields:Error in L.sst[, , i] <- lik.sst[[i]] : number of items to replace is not a multiple of replacement length
which stems from code unique to the parallelized function. Similarly,calc.ohc
yields likelihoods whilecalc.ohc.par
does not (it does not yield an error though).