Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:43 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 908/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
graper 1.20.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: graper |
Version: 1.20.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.20.0.tar.gz |
StartedAt: 2024-06-24 21:52:49 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 21:54:01 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 71.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: graper.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘graper/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘graper’ version ‘1.20.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘graper’ can be installed ... WARNING Found the following significant warnings: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings] # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" See ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ? checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00check.log’ for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘graper’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o In file included from fit_graper.cpp:4: In file included from ./graper_linear_dense_ff.h:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings] # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(graper) > > test_check("graper") iteration 1 Updating parameters of variational distributions... Calculating ELB.. ELB=-868.489 ELB improved by inf iteration 2 Updating parameters of variational distributions... Calculating ELB.. ELB=-558.432 ELB improved by 310.056 iteration 3 Updating parameters of variational distributions... Calculating ELB.. ELB=-496.939 ELB improved by 61.4938 iteration 4 Updating parameters of variational distributions... Calculating ELB.. ELB=-462.489 ELB improved by 34.4496 iteration 5 Updating parameters of variational distributions... Calculating ELB.. ELB=-446.897 ELB improved by 15.5919 iteration 6 Updating parameters of variational distributions... Calculating ELB.. ELB=-438.619 ELB improved by 8.27762 iteration 7 Updating parameters of variational distributions... Calculating ELB.. ELB=-432.542 ELB improved by 6.07743 iteration 8 Updating parameters of variational distributions... Calculating ELB.. ELB=-426.731 ELB improved by 5.8113 iteration 9 Updating parameters of variational distributions... Calculating ELB.. ELB=-420.421 ELB improved by 6.3101 iteration 10 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.263 ELB improved by 7.1579 iteration 11 Updating parameters of variational distributions... Calculating ELB.. ELB=-405.396 ELB improved by 7.86699 iteration 12 Updating parameters of variational distributions... Calculating ELB.. ELB=-397.666 ELB improved by 7.73005 iteration 13 Updating parameters of variational distributions... Calculating ELB.. ELB=-391.251 ELB improved by 6.41492 iteration 14 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.691 ELB improved by 4.55987 iteration 15 Updating parameters of variational distributions... Calculating ELB.. ELB=-383.726 ELB improved by 2.96478 iteration 16 Updating parameters of variational distributions... Calculating ELB.. ELB=-381.846 ELB improved by 1.87987 iteration 17 Updating parameters of variational distributions... Calculating ELB.. ELB=-380.625 ELB improved by 1.22174 iteration 18 Updating parameters of variational distributions... Calculating ELB.. ELB=-379.787 ELB improved by 0.837958 iteration 19 Updating parameters of variational distributions... Calculating ELB.. ELB=-379.177 ELB improved by 0.609981 iteration 20 Updating parameters of variational distributions... Calculating ELB.. ELB=-378.71 ELB improved by 0.467014 iteration 21 Updating parameters of variational distributions... Calculating ELB.. ELB=-378.338 ELB improved by 0.37126 iteration 22 Updating parameters of variational distributions... Calculating ELB.. ELB=-378.035 ELB improved by 0.303186 iteration 23 Updating parameters of variational distributions... Calculating ELB.. ELB=-377.783 ELB improved by 0.252487 iteration 24 Updating parameters of variational distributions... Calculating ELB.. ELB=-377.569 ELB improved by 0.213431 iteration 25 Updating parameters of variational distributions... Calculating ELB.. ELB=-377.387 ELB improved by 0.182599 iteration 26 Updating parameters of variational distributions... Calculating ELB.. ELB=-377.229 ELB improved by 0.157817 iteration 27 Updating parameters of variational distributions... Calculating ELB.. ELB=-377.091 ELB improved by 0.137621 iteration 28 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.97 ELB improved by 0.120984 iteration 29 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.863 ELB improved by 0.107158 iteration 30 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.767 ELB improved by 0.0955862 iteration 31 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.682 ELB improved by 0.0858459 iteration 32 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.604 ELB improved by 0.0776101 iteration 33 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.533 ELB improved by 0.0706234 iteration 34 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.469 ELB improved by 0.0646842 iteration 35 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.409 ELB improved by 0.0596324 iteration 36 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.354 ELB improved by 0.05534 iteration 37 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.302 ELB improved by 0.0517051 iteration 38 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.253 ELB improved by 0.0486465 iteration 39 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.207 ELB improved by 0.0461002 iteration 40 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.163 ELB improved by 0.0440168 iteration 41 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.121 ELB improved by 0.0423596 iteration 42 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.08 ELB improved by 0.041103 iteration 43 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.04 ELB improved by 0.0402321 iteration 44 Updating parameters of variational distributions... Calculating ELB.. ELB=-376 ELB improved by 0.0397421 iteration 45 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.96 ELB improved by 0.0396382 iteration 46 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.92 ELB improved by 0.0399364 iteration 47 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.88 ELB improved by 0.0406648 iteration 48 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.838 ELB improved by 0.0418648 iteration 49 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.794 ELB improved by 0.0435941 iteration 50 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.748 ELB improved by 0.0459303 iteration 51 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.699 ELB improved by 0.0489763 iteration 52 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.646 ELB improved by 0.0528671 iteration 53 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.589 ELB improved by 0.0577808 iteration 54 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.525 ELB improved by 0.0639518 iteration 55 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.453 ELB improved by 0.0716906 iteration 56 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.372 ELB improved by 0.0814092 iteration 57 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.278 ELB improved by 0.0936536 iteration 58 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.169 ELB improved by 0.109141 iteration 59 Updating parameters of variational distributions... Calculating ELB.. ELB=-375.04 ELB improved by 0.128793 iteration 60 Updating parameters of variational distributions... Calculating ELB.. ELB=-374.886 ELB improved by 0.15372 iteration 61 Updating parameters of variational distributions... Calculating ELB.. ELB=-374.701 ELB improved by 0.1851 iteration 62 Updating parameters of variational distributions... Calculating ELB.. ELB=-374.477 ELB improved by 0.223793 iteration 63 Updating parameters of variational distributions... Calculating ELB.. ELB=-374.208 ELB improved by 0.269654 iteration 64 Updating parameters of variational distributions... Calculating ELB.. ELB=-373.887 ELB improved by 0.320823 iteration 65 Updating parameters of variational distributions... Calculating ELB.. ELB=-373.513 ELB improved by 0.373751 iteration 66 Updating parameters of variational distributions... Calculating ELB.. ELB=-373.089 ELB improved by 0.424036 iteration 67 Updating parameters of variational distributions... Calculating ELB.. ELB=-372.622 ELB improved by 0.466778 iteration 68 Updating parameters of variational distributions... Calculating ELB.. ELB=-372.126 ELB improved by 0.496237 iteration 69 Updating parameters of variational distributions... Calculating ELB.. ELB=-371.619 ELB improved by 0.506535 iteration 70 Updating parameters of variational distributions... Calculating ELB.. ELB=-371.126 ELB improved by 0.49388 iteration 71 Updating parameters of variational distributions... Calculating ELB.. ELB=-370.667 ELB improved by 0.458805 iteration 72 Updating parameters of variational distributions... Calculating ELB.. ELB=-370.26 ELB improved by 0.406718 iteration 73 Updating parameters of variational distributions... Calculating ELB.. ELB=-369.914 ELB improved by 0.346165 iteration 74 Updating parameters of variational distributions... Calculating ELB.. ELB=-369.628 ELB improved by 0.285744 iteration 75 Updating parameters of variational distributions... Calculating ELB.. ELB=-369.397 ELB improved by 0.231516 iteration 76 Updating parameters of variational distributions... Calculating ELB.. ELB=-369.21 ELB improved by 0.1862 iteration 77 Updating parameters of variational distributions... Calculating ELB.. ELB=-369.061 ELB improved by 0.149941 iteration 78 Updating parameters of variational distributions... Calculating ELB.. ELB=-368.939 ELB improved by 0.121594 iteration 79 Updating parameters of variational distributions... Calculating ELB.. ELB=-368.839 ELB improved by 0.0996831 iteration 80 Updating parameters of variational distributions... Calculating ELB.. ELB=-368.756 ELB improved by 0.0827818 iteration 81 Updating parameters of variational distributions... Calculating ELB.. ELB=-368.687 ELB improved by 0.0695075 iteration 82 Updating parameters of variational distributions... Calculating ELB.. ELB=-368.628 ELB improved by 0.058474 iteration 83 Updating parameters of variational distributions... Calculating ELB.. ELB=-368.58 ELB improved by 0.048475 iteration 84 Updating parameters of variational distributions... Calculating ELB.. ELB=-368.541 ELB improved by 0.0388914 iteration 85 Updating parameters of variational distributions... Calculating ELB.. ELB=-368.511 ELB improved by 0.0299036 iteration 86 Updating parameters of variational distributions... Calculating ELB.. ELB=-368.489 ELB improved by 0.0221405 iteration 87 Updating parameters of variational distributions... Calculating ELB.. ELB=-368.473 ELB improved by 0.0160634 iteration 88 Updating parameters of variational distributions... Calculating ELB.. ELB=-368.461 ELB improved by 0.011677 iteration 89 Updating parameters of variational distributions... Calculating ELB.. ELB=-368.453 ELB improved by 0.00866155 ELB converged iteration 1 Updating parameters of variational distributions... Calculating ELB.. ELB=-934.301 ELB improved by inf iteration 2 Updating parameters of variational distributions... Calculating ELB.. ELB=-601.103 ELB improved by 333.197 iteration 3 Updating parameters of variational distributions... Calculating ELB.. ELB=-540.684 ELB improved by 60.4197 iteration 4 Updating parameters of variational distributions... Calculating ELB.. ELB=-501.183 ELB improved by 39.5011 iteration 5 Updating parameters of variational distributions... Calculating ELB.. ELB=-483.2 ELB improved by 17.9826 iteration 6 Updating parameters of variational distributions... Calculating ELB.. ELB=-476.149 ELB improved by 7.05099 iteration 7 Updating parameters of variational distributions... Calculating ELB.. ELB=-472.416 ELB improved by 3.73263 iteration 8 Updating parameters of variational distributions... Calculating ELB.. ELB=-469.443 ELB improved by 2.97301 iteration 9 Updating parameters of variational distributions... Calculating ELB.. ELB=-466.608 ELB improved by 2.83565 iteration 10 Updating parameters of variational distributions... Calculating ELB.. ELB=-463.702 ELB improved by 2.9055 iteration 11 Updating parameters of variational distributions... Calculating ELB.. ELB=-460.642 ELB improved by 3.06059 iteration 12 Updating parameters of variational distributions... Calculating ELB.. ELB=-457.47 ELB improved by 3.17178 iteration 13 Updating parameters of variational distributions... Calculating ELB.. ELB=-454.396 ELB improved by 3.07378 iteration 14 Updating parameters of variational distributions... Calculating ELB.. ELB=-451.709 ELB improved by 2.68714 iteration 15 Updating parameters of variational distributions... Calculating ELB.. ELB=-449.577 ELB improved by 2.13206 iteration 16 Updating parameters of variational distributions... Calculating ELB.. ELB=-447.958 ELB improved by 1.6191 iteration 17 Updating parameters of variational distributions... Calculating ELB.. ELB=-446.699 ELB improved by 1.25923 iteration 18 Updating parameters of variational distributions... Calculating ELB.. ELB=-445.652 ELB improved by 1.04616 iteration 19 Updating parameters of variational distributions... Calculating ELB.. ELB=-444.719 ELB improved by 0.933809 iteration 20 Updating parameters of variational distributions... Calculating ELB.. ELB=-443.841 ELB improved by 0.878039 iteration 21 Updating parameters of variational distributions... Calculating ELB.. ELB=-442.992 ELB improved by 0.848702 iteration 22 Updating parameters of variational distributions... Calculating ELB.. ELB=-442.16 ELB improved by 0.831728 iteration 23 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.335 ELB improved by 0.824842 iteration 24 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.502 ELB improved by 0.833137 iteration 25 Updating parameters of variational distributions... Calculating ELB.. ELB=-439.633 ELB improved by 0.86901 iteration 26 Updating parameters of variational distributions... Calculating ELB.. ELB=-438.677 ELB improved by 0.955997 iteration 27 Updating parameters of variational distributions... Calculating ELB.. ELB=-437.556 ELB improved by 1.12145 iteration 28 Updating parameters of variational distributions... Calculating ELB.. ELB=-436.224 ELB improved by 1.33188 iteration 29 Updating parameters of variational distributions... Calculating ELB.. ELB=-434.736 ELB improved by 1.48828 iteration 30 Updating parameters of variational distributions... Calculating ELB.. ELB=-433.132 ELB improved by 1.60389 iteration 31 Updating parameters of variational distributions... Calculating ELB.. ELB=-431.407 ELB improved by 1.72446 iteration 32 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.569 ELB improved by 1.83788 iteration 33 Updating parameters of variational distributions... Calculating ELB.. ELB=-427.639 ELB improved by 1.92999 iteration 34 Updating parameters of variational distributions... Calculating ELB.. ELB=-425.598 ELB improved by 2.04171 iteration 35 Updating parameters of variational distributions... Calculating ELB.. ELB=-423.336 ELB improved by 2.26165 iteration 36 Updating parameters of variational distributions... Calculating ELB.. ELB=-420.87 ELB improved by 2.46548 iteration 37 Updating parameters of variational distributions... Calculating ELB.. ELB=-418.703 ELB improved by 2.16697 iteration 38 Updating parameters of variational distributions... Calculating ELB.. ELB=-417.27 ELB improved by 1.43387 iteration 39 Updating parameters of variational distributions... Calculating ELB.. ELB=-416.398 ELB improved by 0.871413 iteration 40 Updating parameters of variational distributions... Calculating ELB.. ELB=-415.845 ELB improved by 0.553516 iteration 41 Updating parameters of variational distributions... Calculating ELB.. ELB=-415.468 ELB improved by 0.3765 iteration 42 Updating parameters of variational distributions... Calculating ELB.. ELB=-415.196 ELB improved by 0.272458 iteration 43 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.989 ELB improved by 0.20669 iteration 44 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.827 ELB improved by 0.161814 iteration 45 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.698 ELB improved by 0.128982 iteration 46 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.595 ELB improved by 0.103693 iteration 47 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.511 ELB improved by 0.0837045 iteration 48 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.443 ELB improved by 0.0678701 iteration 49 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.388 ELB improved by 0.0554519 iteration 50 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.342 ELB improved by 0.0458125 iteration 51 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.303 ELB improved by 0.0383532 iteration 52 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.271 ELB improved by 0.0325481 iteration 53 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.243 ELB improved by 0.0279749 iteration 54 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.219 ELB improved by 0.0243172 iteration 55 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.197 ELB improved by 0.0213472 iteration 56 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.178 ELB improved by 0.0189026 iteration 57 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.161 ELB improved by 0.0168677 iteration 58 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.146 ELB improved by 0.0151581 iteration 59 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.133 ELB improved by 0.0137111 iteration 60 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.12 ELB improved by 0.012479 iteration 61 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.109 ELB improved by 0.0114243 iteration 62 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.098 ELB improved by 0.0105176 iteration 63 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.088 ELB improved by 0.00973486 ELB converged iteration 1 Updating parameters of variational distributions... Calculating ELB.. ELB=-873.908 ELB improved by inf iteration 2 Updating parameters of variational distributions... Calculating ELB.. ELB=-581.745 ELB improved by 292.164 iteration 3 Updating parameters of variational distributions... Calculating ELB.. ELB=-518.679 ELB improved by 63.066 iteration 4 Updating parameters of variational distributions... Calculating ELB.. ELB=-477.006 ELB improved by 41.6727 iteration 5 Updating parameters of variational distributions... Calculating ELB.. ELB=-459.604 ELB improved by 17.4024 iteration 6 Updating parameters of variational distributions... Calculating ELB.. ELB=-452.306 ELB improved by 7.29714 iteration 7 Updating parameters of variational distributions... Calculating ELB.. ELB=-447.23 ELB improved by 5.07659 iteration 8 Updating parameters of variational distributions... Calculating ELB.. ELB=-442.374 ELB improved by 4.8559 iteration 9 Updating parameters of variational distributions... Calculating ELB.. ELB=-437.294 ELB improved by 5.08002 iteration 10 Updating parameters of variational distributions... Calculating ELB.. ELB=-432.057 ELB improved by 5.23648 iteration 11 Updating parameters of variational distributions... Calculating ELB.. ELB=-427.092 ELB improved by 4.96546 iteration 12 Updating parameters of variational distributions... Calculating ELB.. ELB=-422.94 ELB improved by 4.15155 iteration 13 Updating parameters of variational distributions... Calculating ELB.. ELB=-419.878 ELB improved by 3.06268 iteration 14 Updating parameters of variational distributions... Calculating ELB.. ELB=-417.785 ELB improved by 2.0927 iteration 15 Updating parameters of variational distributions... Calculating ELB.. ELB=-416.34 ELB improved by 1.44544 iteration 16 Updating parameters of variational distributions... Calculating ELB.. ELB=-415.239 ELB improved by 1.10113 iteration 17 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.273 ELB improved by 0.966 iteration 18 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.317 ELB improved by 0.955608 iteration 19 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.326 ELB improved by 0.991311 iteration 20 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.271 ELB improved by 1.0547 iteration 21 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.09 ELB improved by 1.18133 iteration 22 Updating parameters of variational distributions... Calculating ELB.. ELB=-408.759 ELB improved by 1.33083 iteration 23 Updating parameters of variational distributions... Calculating ELB.. ELB=-407.326 ELB improved by 1.43264 iteration 24 Updating parameters of variational distributions... Calculating ELB.. ELB=-405.811 ELB improved by 1.51534 iteration 25 Updating parameters of variational distributions... Calculating ELB.. ELB=-404.172 ELB improved by 1.63849 iteration 26 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.31 ELB improved by 1.86189 iteration 27 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.095 ELB improved by 2.21558 iteration 28 Updating parameters of variational distributions... Calculating ELB.. ELB=-397.428 ELB improved by 2.66711 iteration 29 Updating parameters of variational distributions... Calculating ELB.. ELB=-394.323 ELB improved by 3.10495 iteration 30 Updating parameters of variational distributions... Calculating ELB.. ELB=-390.938 ELB improved by 3.38449 iteration 31 Updating parameters of variational distributions... Calculating ELB.. ELB=-387.578 ELB improved by 3.35988 iteration 32 Updating parameters of variational distributions... Calculating ELB.. ELB=-384.576 ELB improved by 3.00245 iteration 33 Updating parameters of variational distributions... Calculating ELB.. ELB=-382.151 ELB improved by 2.42467 iteration 34 Updating parameters of variational distributions... Calculating ELB.. ELB=-380.409 ELB improved by 1.74197 iteration 35 Updating parameters of variational distributions... Calculating ELB.. ELB=-379.227 ELB improved by 1.18181 iteration 36 Updating parameters of variational distributions... Calculating ELB.. ELB=-378.399 ELB improved by 0.828405 iteration 37 Updating parameters of variational distributions... Calculating ELB.. ELB=-377.815 ELB improved by 0.58425 iteration 38 Updating parameters of variational distributions... Calculating ELB.. ELB=-377.419 ELB improved by 0.395333 iteration 39 Updating parameters of variational distributions... Calculating ELB.. ELB=-377.154 ELB improved by 0.265792 iteration 40 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.967 ELB improved by 0.186341 iteration 41 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.83 ELB improved by 0.137112 iteration 42 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.726 ELB improved by 0.104547 iteration 43 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.644 ELB improved by 0.0816746 iteration 44 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.579 ELB improved by 0.064938 iteration 45 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.527 ELB improved by 0.0523588 iteration 46 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.484 ELB improved by 0.042726 iteration 47 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.449 ELB improved by 0.0352445 iteration 48 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.419 ELB improved by 0.0293668 iteration 49 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.395 ELB improved by 0.0247039 iteration 50 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.374 ELB improved by 0.0209729 iteration 51 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.356 ELB improved by 0.0179648 iteration 52 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.34 ELB improved by 0.0155226 iteration 53 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.327 ELB improved by 0.0135271 iteration 54 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.315 ELB improved by 0.0118868 iteration 55 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.304 ELB improved by 0.0105308 iteration 56 Updating parameters of variational distributions... Calculating ELB.. ELB=-376.295 ELB improved by 0.00940372 ELB converged iteration 1 Updating parameters of variational distributions... Calculating ELB.. ELB=-862.235 ELB improved by inf iteration 2 Updating parameters of variational distributions... Calculating ELB.. ELB=-587.859 ELB improved by 274.376 iteration 3 Updating parameters of variational distributions... Calculating ELB.. ELB=-525.094 ELB improved by 62.7651 iteration 4 Updating parameters of variational distributions... Calculating ELB.. ELB=-481.051 ELB improved by 44.0427 iteration 5 Updating parameters of variational distributions... Calculating ELB.. ELB=-460.726 ELB improved by 20.325 iteration 6 Updating parameters of variational distributions... Calculating ELB.. ELB=-452.056 ELB improved by 8.67068 iteration 7 Updating parameters of variational distributions... Calculating ELB.. ELB=-446.476 ELB improved by 5.57997 iteration 8 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.59 ELB improved by 4.88582 iteration 9 Updating parameters of variational distributions... Calculating ELB.. ELB=-436.777 ELB improved by 4.81272 iteration 10 Updating parameters of variational distributions... Calculating ELB.. ELB=-431.982 ELB improved by 4.79553 iteration 11 Updating parameters of variational distributions... Calculating ELB.. ELB=-427.459 ELB improved by 4.52215 iteration 12 Updating parameters of variational distributions... Calculating ELB.. ELB=-423.578 ELB improved by 3.88131 iteration 13 Updating parameters of variational distributions... Calculating ELB.. ELB=-420.562 ELB improved by 3.01564 iteration 14 Updating parameters of variational distributions... Calculating ELB.. ELB=-418.386 ELB improved by 2.17697 iteration 15 Updating parameters of variational distributions... Calculating ELB.. ELB=-416.86 ELB improved by 1.52588 iteration 16 Updating parameters of variational distributions... Calculating ELB.. ELB=-415.775 ELB improved by 1.08456 iteration 17 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.972 ELB improved by 0.80339 iteration 18 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.347 ELB improved by 0.624272 iteration 19 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.843 ELB improved by 0.504488 iteration 20 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.426 ELB improved by 0.417384 iteration 21 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.078 ELB improved by 0.347648 iteration 22 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.79 ELB improved by 0.287981 iteration 23 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.553 ELB improved by 0.236609 iteration 24 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.359 ELB improved by 0.194079 iteration 25 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.199 ELB improved by 0.160462 iteration 26 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.064 ELB improved by 0.134577 iteration 27 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.95 ELB improved by 0.114651 iteration 28 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.85 ELB improved by 0.099041 iteration 29 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.764 ELB improved by 0.0865153 iteration 30 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.688 ELB improved by 0.0762353 iteration 31 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.62 ELB improved by 0.0676427 iteration 32 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.56 ELB improved by 0.0603595 iteration 33 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.506 ELB improved by 0.0541199 iteration 34 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.457 ELB improved by 0.0487296 iteration 35 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.413 ELB improved by 0.0440412 iteration 36 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.373 ELB improved by 0.0399399 iteration 37 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.337 ELB improved by 0.0363342 iteration 38 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.303 ELB improved by 0.0331503 iteration 39 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.273 ELB improved by 0.0303276 iteration 40 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.245 ELB improved by 0.0278162 iteration 41 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.22 ELB improved by 0.0255745 iteration 42 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.196 ELB improved by 0.0235674 iteration 43 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.174 ELB improved by 0.0217656 iteration 44 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.154 ELB improved by 0.0201438 iteration 45 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.136 ELB improved by 0.0186808 iteration 46 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.118 ELB improved by 0.0173582 iteration 47 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.102 ELB improved by 0.01616 iteration 48 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.087 ELB improved by 0.0150727 iteration 49 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.073 ELB improved by 0.0140843 iteration 50 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.06 ELB improved by 0.0131844 iteration 51 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.047 ELB improved by 0.012364 iteration 52 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.036 ELB improved by 0.011615 iteration 53 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.025 ELB improved by 0.0109305 iteration 54 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.014 ELB improved by 0.0103042 iteration 55 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.005 ELB improved by 0.00973067 ELB converged [ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ] > > proc.time() user system elapsed 2.769 0.223 3.015
graper.Rcheck/graper-Ex.timings
name | user | system | elapsed | |
coef.graper | 0.091 | 0.016 | 0.106 | |
getPIPs | 0.083 | 0.013 | 0.097 | |
graper | 0.136 | 0.018 | 0.153 | |
makeExampleData | 0.013 | 0.001 | 0.014 | |
makeExampleDataWithUnequalGroups | 0.037 | 0.003 | 0.040 | |
plotELBO | 0.268 | 0.018 | 0.287 | |
plotGroupPenalties | 0.769 | 0.024 | 0.797 | |
plotPosterior | 0.616 | 0.019 | 0.636 | |
predict.graper | 3.096 | 0.082 | 3.187 | |
print.graper | 0.082 | 0.011 | 0.093 | |