Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-03 11:38:25 -0400 (Fri, 03 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
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 878/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
graper 1.21.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | 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 | see weekly results here | ||||||||||||
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: 1.21.0 |
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_1.21.0.tar.gz |
StartedAt: 2024-05-02 05:20:42 -0400 (Thu, 02 May 2024) |
EndedAt: 2024-05-02 05:22:57 -0400 (Thu, 02 May 2024) |
EllapsedTime: 135.0 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_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-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 Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘graper/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘graper’ version ‘1.21.0’ * 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-x86_64/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-3.20-bioc/meat/graper.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * 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-3.20-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-x86_64/Resources/library’ * installing *source* package ‘graper’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/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-x86_64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11: /Library/Frameworks/R.framework/Versions/4.4-x86_64/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 x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/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 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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=-855.747 ELB improved by inf iteration 2 Updating parameters of variational distributions... Calculating ELB.. ELB=-567.968 ELB improved by 287.779 iteration 3 Updating parameters of variational distributions... Calculating ELB.. ELB=-509.486 ELB improved by 58.4816 iteration 4 Updating parameters of variational distributions... Calculating ELB.. ELB=-474.257 ELB improved by 35.2294 iteration 5 Updating parameters of variational distributions... Calculating ELB.. ELB=-459.723 ELB improved by 14.5341 iteration 6 Updating parameters of variational distributions... Calculating ELB.. ELB=-453.836 ELB improved by 5.88698 iteration 7 Updating parameters of variational distributions... Calculating ELB.. ELB=-450.161 ELB improved by 3.6751 iteration 8 Updating parameters of variational distributions... Calculating ELB.. ELB=-446.924 ELB improved by 3.23649 iteration 9 Updating parameters of variational distributions... Calculating ELB.. ELB=-443.607 ELB improved by 3.31671 iteration 10 Updating parameters of variational distributions... Calculating ELB.. ELB=-439.959 ELB improved by 3.64851 iteration 11 Updating parameters of variational distributions... Calculating ELB.. ELB=-435.856 ELB improved by 4.10324 iteration 12 Updating parameters of variational distributions... Calculating ELB.. ELB=-431.347 ELB improved by 4.50893 iteration 13 Updating parameters of variational distributions... Calculating ELB.. ELB=-426.77 ELB improved by 4.5771 iteration 14 Updating parameters of variational distributions... Calculating ELB.. ELB=-422.672 ELB improved by 4.09782 iteration 15 Updating parameters of variational distributions... Calculating ELB.. ELB=-419.465 ELB improved by 3.20687 iteration 16 Updating parameters of variational distributions... Calculating ELB.. ELB=-417.177 ELB improved by 2.28832 iteration 17 Updating parameters of variational distributions... Calculating ELB.. ELB=-415.546 ELB improved by 1.63102 iteration 18 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.273 ELB improved by 1.27237 iteration 19 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.145 ELB improved by 1.12878 iteration 20 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.028 ELB improved by 1.11665 iteration 21 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.845 ELB improved by 1.18279 iteration 22 Updating parameters of variational distributions... Calculating ELB.. ELB=-409.546 ELB improved by 1.2987 iteration 23 Updating parameters of variational distributions... Calculating ELB.. ELB=-408.096 ELB improved by 1.45057 iteration 24 Updating parameters of variational distributions... Calculating ELB.. ELB=-406.466 ELB improved by 1.62981 iteration 25 Updating parameters of variational distributions... Calculating ELB.. ELB=-404.644 ELB improved by 1.82185 iteration 26 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.651 ELB improved by 1.9932 iteration 27 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.564 ELB improved by 2.08666 iteration 28 Updating parameters of variational distributions... Calculating ELB.. ELB=-398.524 ELB improved by 2.04034 iteration 29 Updating parameters of variational distributions... Calculating ELB.. ELB=-396.695 ELB improved by 1.82936 iteration 30 Updating parameters of variational distributions... Calculating ELB.. ELB=-395.199 ELB improved by 1.49596 iteration 31 Updating parameters of variational distributions... Calculating ELB.. ELB=-394.068 ELB improved by 1.13114 iteration 32 Updating parameters of variational distributions... Calculating ELB.. ELB=-393.251 ELB improved by 0.816939 iteration 33 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.665 ELB improved by 0.585693 iteration 34 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.237 ELB improved by 0.427966 iteration 35 Updating parameters of variational distributions... Calculating ELB.. ELB=-391.916 ELB improved by 0.321177 iteration 36 Updating parameters of variational distributions... Calculating ELB.. ELB=-391.669 ELB improved by 0.246956 iteration 37 Updating parameters of variational distributions... Calculating ELB.. ELB=-391.474 ELB improved by 0.194647 iteration 38 Updating parameters of variational distributions... Calculating ELB.. ELB=-391.315 ELB improved by 0.158998 iteration 39 Updating parameters of variational distributions... Calculating ELB.. ELB=-391.178 ELB improved by 0.137532 iteration 40 Updating parameters of variational distributions... Calculating ELB.. ELB=-391.048 ELB improved by 0.129649 iteration 41 Updating parameters of variational distributions... Calculating ELB.. ELB=-390.911 ELB improved by 0.136648 iteration 42 Updating parameters of variational distributions... Calculating ELB.. ELB=-390.752 ELB improved by 0.159212 iteration 43 Updating parameters of variational distributions... Calculating ELB.. ELB=-390.564 ELB improved by 0.187715 iteration 44 Updating parameters of variational distributions... Calculating ELB.. ELB=-390.364 ELB improved by 0.200858 iteration 45 Updating parameters of variational distributions... Calculating ELB.. ELB=-390.158 ELB improved by 0.205665 iteration 46 Updating parameters of variational distributions... Calculating ELB.. ELB=-389.9 ELB improved by 0.257482 iteration 47 Updating parameters of variational distributions... Calculating ELB.. ELB=-389.487 ELB improved by 0.413218 iteration 48 Updating parameters of variational distributions... Calculating ELB.. ELB=-388.903 ELB improved by 0.583984 iteration 49 Updating parameters of variational distributions... Calculating ELB.. ELB=-388.385 ELB improved by 0.517732 iteration 50 Updating parameters of variational distributions... Calculating ELB.. ELB=-388.058 ELB improved by 0.32698 iteration 51 Updating parameters of variational distributions... Calculating ELB.. ELB=-387.848 ELB improved by 0.210909 iteration 52 Updating parameters of variational distributions... Calculating ELB.. ELB=-387.679 ELB improved by 0.168104 iteration 53 Updating parameters of variational distributions... Calculating ELB.. ELB=-387.524 ELB improved by 0.155634 iteration 54 Updating parameters of variational distributions... Calculating ELB.. ELB=-387.379 ELB improved by 0.144532 iteration 55 Updating parameters of variational distributions... Calculating ELB.. ELB=-387.252 ELB improved by 0.127702 iteration 56 Updating parameters of variational distributions... Calculating ELB.. ELB=-387.141 ELB improved by 0.110772 iteration 57 Updating parameters of variational distributions... Calculating ELB.. ELB=-387.045 ELB improved by 0.095464 iteration 58 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.966 ELB improved by 0.0795627 iteration 59 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.902 ELB improved by 0.0633407 iteration 60 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.853 ELB improved by 0.049239 iteration 61 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.815 ELB improved by 0.0383787 iteration 62 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.785 ELB improved by 0.0301009 iteration 63 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.761 ELB improved by 0.0234722 iteration 64 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.743 ELB improved by 0.018057 iteration 65 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.729 ELB improved by 0.0137743 iteration 66 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.719 ELB improved by 0.0105761 iteration 67 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.711 ELB improved by 0.00831469 ELB converged iteration 1 Updating parameters of variational distributions... Calculating ELB.. ELB=-862.012 ELB improved by inf iteration 2 Updating parameters of variational distributions... Calculating ELB.. ELB=-571.306 ELB improved by 290.706 iteration 3 Updating parameters of variational distributions... Calculating ELB.. ELB=-507.745 ELB improved by 63.5606 iteration 4 Updating parameters of variational distributions... Calculating ELB.. ELB=-469.074 ELB improved by 38.671 iteration 5 Updating parameters of variational distributions... Calculating ELB.. ELB=-453.681 ELB improved by 15.3927 iteration 6 Updating parameters of variational distributions... Calculating ELB.. ELB=-446.983 ELB improved by 6.69845 iteration 7 Updating parameters of variational distributions... Calculating ELB.. ELB=-442.572 ELB improved by 4.41078 iteration 8 Updating parameters of variational distributions... Calculating ELB.. ELB=-438.804 ELB improved by 3.7678 iteration 9 Updating parameters of variational distributions... Calculating ELB.. ELB=-435.138 ELB improved by 3.66593 iteration 10 Updating parameters of variational distributions... Calculating ELB.. ELB=-431.425 ELB improved by 3.71368 iteration 11 Updating parameters of variational distributions... Calculating ELB.. ELB=-427.75 ELB improved by 3.6744 iteration 12 Updating parameters of variational distributions... Calculating ELB.. ELB=-424.358 ELB improved by 3.39181 iteration 13 Updating parameters of variational distributions... Calculating ELB.. ELB=-421.521 ELB improved by 2.83733 iteration 14 Updating parameters of variational distributions... Calculating ELB.. ELB=-419.374 ELB improved by 2.14688 iteration 15 Updating parameters of variational distributions... Calculating ELB.. ELB=-417.857 ELB improved by 1.51755 iteration 16 Updating parameters of variational distributions... Calculating ELB.. ELB=-416.792 ELB improved by 1.06428 iteration 17 Updating parameters of variational distributions... Calculating ELB.. ELB=-416.004 ELB improved by 0.788538 iteration 18 Updating parameters of variational distributions... Calculating ELB.. ELB=-415.368 ELB improved by 0.635387 iteration 19 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.825 ELB improved by 0.543267 iteration 20 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.36 ELB improved by 0.465396 iteration 21 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.976 ELB improved by 0.383451 iteration 22 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.672 ELB improved by 0.303948 iteration 23 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.435 ELB improved by 0.237644 iteration 24 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.247 ELB improved by 0.187917 iteration 25 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.094 ELB improved by 0.1523 iteration 26 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.968 ELB improved by 0.12678 iteration 27 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.86 ELB improved by 0.108004 iteration 28 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.766 ELB improved by 0.0936919 iteration 29 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.684 ELB improved by 0.0824092 iteration 30 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.61 ELB improved by 0.0732663 iteration 31 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.545 ELB improved by 0.0657002 iteration 32 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.485 ELB improved by 0.0593407 iteration 33 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.431 ELB improved by 0.0539337 iteration 34 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.382 ELB improved by 0.0492967 iteration 35 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.337 ELB improved by 0.045294 iteration 36 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.295 ELB improved by 0.0418217 iteration 37 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.256 ELB improved by 0.0387979 iteration 38 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.22 ELB improved by 0.0361575 iteration 39 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.186 ELB improved by 0.0338476 iteration 40 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.154 ELB improved by 0.0318247 iteration 41 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.124 ELB improved by 0.030053 iteration 42 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.096 ELB improved by 0.0285027 iteration 43 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.069 ELB improved by 0.027149 iteration 44 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.043 ELB improved by 0.0259711 iteration 45 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.018 ELB improved by 0.0249515 iteration 46 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.994 ELB improved by 0.0240756 iteration 47 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.97 ELB improved by 0.0233313 iteration 48 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.948 ELB improved by 0.0227086 iteration 49 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.925 ELB improved by 0.0221992 iteration 50 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.904 ELB improved by 0.0217967 iteration 51 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.882 ELB improved by 0.0214962 iteration 52 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.861 ELB improved by 0.021294 iteration 53 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.84 ELB improved by 0.0211882 iteration 54 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.818 ELB improved by 0.021178 iteration 55 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.797 ELB improved by 0.0212643 iteration 56 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.776 ELB improved by 0.0214494 iteration 57 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.754 ELB improved by 0.0217375 iteration 58 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.732 ELB improved by 0.0221345 iteration 59 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.709 ELB improved by 0.0226489 iteration 60 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.686 ELB improved by 0.0232918 iteration 61 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.662 ELB improved by 0.0240779 iteration 62 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.637 ELB improved by 0.0250258 iteration 63 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.611 ELB improved by 0.0261597 iteration 64 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.583 ELB improved by 0.0275104 iteration 65 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.554 ELB improved by 0.0291179 iteration 66 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.523 ELB improved by 0.0310333 iteration 67 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.49 ELB improved by 0.0333233 iteration 68 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.454 ELB improved by 0.0360746 iteration 69 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.414 ELB improved by 0.0394001 iteration 70 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.371 ELB improved by 0.0434471 iteration 71 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.322 ELB improved by 0.0484064 iteration 72 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.268 ELB improved by 0.0545215 iteration 73 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.206 ELB improved by 0.0620942 iteration 74 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.134 ELB improved by 0.0714821 iteration 75 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.051 ELB improved by 0.0830769 iteration 76 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.954 ELB improved by 0.0972614 iteration 77 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.84 ELB improved by 0.114353 iteration 78 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.705 ELB improved by 0.134575 iteration 79 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.547 ELB improved by 0.158112 iteration 80 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.362 ELB improved by 0.185266 iteration 81 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.145 ELB improved by 0.216629 iteration 82 Updating parameters of variational distributions... Calculating ELB.. ELB=-409.892 ELB improved by 0.253163 iteration 83 Updating parameters of variational distributions... Calculating ELB.. ELB=-409.596 ELB improved by 0.296145 iteration 84 Updating parameters of variational distributions... Calculating ELB.. ELB=-409.249 ELB improved by 0.346994 iteration 85 Updating parameters of variational distributions... Calculating ELB.. ELB=-408.842 ELB improved by 0.406813 iteration 86 Updating parameters of variational distributions... Calculating ELB.. ELB=-408.367 ELB improved by 0.475325 iteration 87 Updating parameters of variational distributions... Calculating ELB.. ELB=-407.818 ELB improved by 0.548947 iteration 88 Updating parameters of variational distributions... Calculating ELB.. ELB=-407.198 ELB improved by 0.619118 iteration 89 Updating parameters of variational distributions... Calculating ELB.. ELB=-406.525 ELB improved by 0.673635 iteration 90 Updating parameters of variational distributions... Calculating ELB.. ELB=-405.823 ELB improved by 0.701864 iteration 91 Updating parameters of variational distributions... Calculating ELB.. ELB=-405.123 ELB improved by 0.700315 iteration 92 Updating parameters of variational distributions... Calculating ELB.. ELB=-404.447 ELB improved by 0.675517 iteration 93 Updating parameters of variational distributions... Calculating ELB.. ELB=-403.807 ELB improved by 0.639895 iteration 94 Updating parameters of variational distributions... Calculating ELB.. ELB=-403.211 ELB improved by 0.596269 iteration 95 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.68 ELB improved by 0.531227 iteration 96 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.238 ELB improved by 0.442129 iteration 97 Updating parameters of variational distributions... Calculating ELB.. ELB=-401.889 ELB improved by 0.348651 iteration 98 Updating parameters of variational distributions... Calculating ELB.. ELB=-401.619 ELB improved by 0.269949 iteration 99 Updating parameters of variational distributions... Calculating ELB.. ELB=-401.404 ELB improved by 0.214845 iteration 100 Updating parameters of variational distributions... Calculating ELB.. ELB=-401.22 ELB improved by 0.184312 iteration 101 Updating parameters of variational distributions... Calculating ELB.. ELB=-401.044 ELB improved by 0.175511 iteration 102 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.862 ELB improved by 0.182164 iteration 103 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.673 ELB improved by 0.188701 iteration 104 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.503 ELB improved by 0.17074 iteration 105 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.38 ELB improved by 0.123155 iteration 106 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.306 ELB improved by 0.0732239 iteration 107 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.265 ELB improved by 0.0409914 iteration 108 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.241 ELB improved by 0.0241807 iteration 109 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.226 ELB improved by 0.0155478 iteration 110 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.215 ELB improved by 0.0108219 iteration 111 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.207 ELB improved by 0.00805527 ELB converged iteration 1 Updating parameters of variational distributions... Calculating ELB.. ELB=-921.245 ELB improved by inf iteration 2 Updating parameters of variational distributions... Calculating ELB.. ELB=-578.965 ELB improved by 342.28 iteration 3 Updating parameters of variational distributions... Calculating ELB.. ELB=-519.953 ELB improved by 59.0125 iteration 4 Updating parameters of variational distributions... Calculating ELB.. ELB=-488.424 ELB improved by 31.5292 iteration 5 Updating parameters of variational distributions... Calculating ELB.. ELB=-474.815 ELB improved by 13.609 iteration 6 Updating parameters of variational distributions... Calculating ELB.. ELB=-467.905 ELB improved by 6.90921 iteration 7 Updating parameters of variational distributions... Calculating ELB.. ELB=-463.045 ELB improved by 4.85991 iteration 8 Updating parameters of variational distributions... Calculating ELB.. ELB=-458.72 ELB improved by 4.32492 iteration 9 Updating parameters of variational distributions... Calculating ELB.. ELB=-454.377 ELB improved by 4.34316 iteration 10 Updating parameters of variational distributions... Calculating ELB.. ELB=-449.891 ELB improved by 4.48666 iteration 11 Updating parameters of variational distributions... Calculating ELB.. ELB=-445.495 ELB improved by 4.39526 iteration 12 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.672 ELB improved by 3.82316 iteration 13 Updating parameters of variational distributions... Calculating ELB.. ELB=-438.741 ELB improved by 2.93101 iteration 14 Updating parameters of variational distributions... Calculating ELB.. ELB=-436.628 ELB improved by 2.11303 iteration 15 Updating parameters of variational distributions... Calculating ELB.. ELB=-435.072 ELB improved by 1.55588 iteration 16 Updating parameters of variational distributions... Calculating ELB.. ELB=-433.881 ELB improved by 1.1915 iteration 17 Updating parameters of variational distributions... Calculating ELB.. ELB=-432.972 ELB improved by 0.908981 iteration 18 Updating parameters of variational distributions... Calculating ELB.. ELB=-432.294 ELB improved by 0.677398 iteration 19 Updating parameters of variational distributions... Calculating ELB.. ELB=-431.789 ELB improved by 0.505733 iteration 20 Updating parameters of variational distributions... Calculating ELB.. ELB=-431.401 ELB improved by 0.387882 iteration 21 Updating parameters of variational distributions... Calculating ELB.. ELB=-431.093 ELB improved by 0.307504 iteration 22 Updating parameters of variational distributions... Calculating ELB.. ELB=-430.843 ELB improved by 0.25083 iteration 23 Updating parameters of variational distributions... Calculating ELB.. ELB=-430.633 ELB improved by 0.209102 iteration 24 Updating parameters of variational distributions... Calculating ELB.. ELB=-430.456 ELB improved by 0.177171 iteration 25 Updating parameters of variational distributions... Calculating ELB.. ELB=-430.304 ELB improved by 0.151995 iteration 26 Updating parameters of variational distributions... Calculating ELB.. ELB=-430.173 ELB improved by 0.131697 iteration 27 Updating parameters of variational distributions... Calculating ELB.. ELB=-430.057 ELB improved by 0.11505 iteration 28 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.956 ELB improved by 0.101212 iteration 29 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.867 ELB improved by 0.0895824 iteration 30 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.787 ELB improved by 0.0797159 iteration 31 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.716 ELB improved by 0.0712765 iteration 32 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.652 ELB improved by 0.0640055 iteration 33 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.594 ELB improved by 0.0577005 iteration 34 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.542 ELB improved by 0.0522012 iteration 35 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.494 ELB improved by 0.0473794 iteration 36 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.451 ELB improved by 0.0431311 iteration 37 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.412 ELB improved by 0.0393717 iteration 38 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.376 ELB improved by 0.0360315 iteration 39 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.343 ELB improved by 0.0330528 iteration 40 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.312 ELB improved by 0.0303872 iteration 41 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.284 ELB improved by 0.0279944 iteration 42 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.259 ELB improved by 0.0258402 iteration 43 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.235 ELB improved by 0.0238954 iteration 44 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.213 ELB improved by 0.0221353 iteration 45 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.192 ELB improved by 0.0205386 iteration 46 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.173 ELB improved by 0.019087 iteration 47 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.155 ELB improved by 0.0177645 iteration 48 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.139 ELB improved by 0.0165573 iteration 49 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.123 ELB improved by 0.0154534 iteration 50 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.109 ELB improved by 0.0144423 iteration 51 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.095 ELB improved by 0.0135145 iteration 52 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.083 ELB improved by 0.0126621 iteration 53 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.071 ELB improved by 0.0118777 iteration 54 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.06 ELB improved by 0.0111549 iteration 55 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.049 ELB improved by 0.0104881 iteration 56 Updating parameters of variational distributions... Calculating ELB.. ELB=-429.039 ELB improved by 0.00987208 ELB converged iteration 1 Updating parameters of variational distributions... Calculating ELB.. ELB=-839.307 ELB improved by inf iteration 2 Updating parameters of variational distributions... Calculating ELB.. ELB=-582.224 ELB improved by 257.083 iteration 3 Updating parameters of variational distributions... Calculating ELB.. ELB=-522.948 ELB improved by 59.2766 iteration 4 Updating parameters of variational distributions... Calculating ELB.. ELB=-480.161 ELB improved by 42.7865 iteration 5 Updating parameters of variational distributions... Calculating ELB.. ELB=-459.439 ELB improved by 20.7219 iteration 6 Updating parameters of variational distributions... Calculating ELB.. ELB=-451.392 ELB improved by 8.04753 iteration 7 Updating parameters of variational distributions... Calculating ELB.. ELB=-446.939 ELB improved by 4.45215 iteration 8 Updating parameters of variational distributions... Calculating ELB.. ELB=-443.513 ELB improved by 3.4269 iteration 9 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.244 ELB improved by 3.2684 iteration 10 Updating parameters of variational distributions... Calculating ELB.. ELB=-436.736 ELB improved by 3.50848 iteration 11 Updating parameters of variational distributions... Calculating ELB.. ELB=-432.85 ELB improved by 3.88541 iteration 12 Updating parameters of variational distributions... Calculating ELB.. ELB=-428.698 ELB improved by 4.15222 iteration 13 Updating parameters of variational distributions... Calculating ELB.. ELB=-424.638 ELB improved by 4.05961 iteration 14 Updating parameters of variational distributions... Calculating ELB.. ELB=-421.087 ELB improved by 3.5516 iteration 15 Updating parameters of variational distributions... Calculating ELB.. ELB=-418.227 ELB improved by 2.8601 iteration 16 Updating parameters of variational distributions... Calculating ELB.. ELB=-416.03 ELB improved by 2.19639 iteration 17 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.462 ELB improved by 1.56804 iteration 18 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.391 ELB improved by 1.07114 iteration 19 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.63 ELB improved by 0.760934 iteration 20 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.047 ELB improved by 0.583518 iteration 21 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.568 ELB improved by 0.478688 iteration 22 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.158 ELB improved by 0.409852 iteration 23 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.798 ELB improved by 0.360225 iteration 24 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.474 ELB improved by 0.324148 iteration 25 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.175 ELB improved by 0.299251 iteration 26 Updating parameters of variational distributions... Calculating ELB.. ELB=-409.891 ELB improved by 0.283119 iteration 27 Updating parameters of variational distributions... Calculating ELB.. ELB=-409.618 ELB improved by 0.273396 iteration 28 Updating parameters of variational distributions... Calculating ELB.. ELB=-409.35 ELB improved by 0.268347 iteration 29 Updating parameters of variational distributions... Calculating ELB.. ELB=-409.083 ELB improved by 0.266922 iteration 30 Updating parameters of variational distributions... Calculating ELB.. ELB=-408.814 ELB improved by 0.268609 iteration 31 Updating parameters of variational distributions... Calculating ELB.. ELB=-408.541 ELB improved by 0.273323 iteration 32 Updating parameters of variational distributions... Calculating ELB.. ELB=-408.259 ELB improved by 0.281369 iteration 33 Updating parameters of variational distributions... Calculating ELB.. ELB=-407.966 ELB improved by 0.29349 iteration 34 Updating parameters of variational distributions... Calculating ELB.. ELB=-407.655 ELB improved by 0.311006 iteration 35 Updating parameters of variational distributions... Calculating ELB.. ELB=-407.319 ELB improved by 0.336099 iteration 36 Updating parameters of variational distributions... Calculating ELB.. ELB=-406.947 ELB improved by 0.372345 iteration 37 Updating parameters of variational distributions... Calculating ELB.. ELB=-406.521 ELB improved by 0.425627 iteration 38 Updating parameters of variational distributions... Calculating ELB.. ELB=-406.016 ELB improved by 0.505305 iteration 39 Updating parameters of variational distributions... Calculating ELB.. ELB=-405.391 ELB improved by 0.624083 iteration 40 Updating parameters of variational distributions... Calculating ELB.. ELB=-404.6 ELB improved by 0.791419 iteration 41 Updating parameters of variational distributions... Calculating ELB.. ELB=-403.605 ELB improved by 0.994812 iteration 42 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.427 ELB improved by 1.1787 iteration 43 Updating parameters of variational distributions... Calculating ELB.. ELB=-401.153 ELB improved by 1.27338 iteration 44 Updating parameters of variational distributions... Calculating ELB.. ELB=-399.877 ELB improved by 1.27602 iteration 45 Updating parameters of variational distributions... Calculating ELB.. ELB=-398.658 ELB improved by 1.21889 iteration 46 Updating parameters of variational distributions... Calculating ELB.. ELB=-397.539 ELB improved by 1.11976 iteration 47 Updating parameters of variational distributions... Calculating ELB.. ELB=-396.543 ELB improved by 0.995017 iteration 48 Updating parameters of variational distributions... Calculating ELB.. ELB=-395.692 ELB improved by 0.85176 iteration 49 Updating parameters of variational distributions... Calculating ELB.. ELB=-395.003 ELB improved by 0.688498 iteration 50 Updating parameters of variational distributions... Calculating ELB.. ELB=-394.482 ELB improved by 0.521319 iteration 51 Updating parameters of variational distributions... Calculating ELB.. ELB=-394.103 ELB improved by 0.379391 iteration 52 Updating parameters of variational distributions... Calculating ELB.. ELB=-393.826 ELB improved by 0.276927 iteration 53 Updating parameters of variational distributions... Calculating ELB.. ELB=-393.615 ELB improved by 0.210447 iteration 54 Updating parameters of variational distributions... Calculating ELB.. ELB=-393.445 ELB improved by 0.169691 iteration 55 Updating parameters of variational distributions... Calculating ELB.. ELB=-393.302 ELB improved by 0.143833 iteration 56 Updating parameters of variational distributions... Calculating ELB.. ELB=-393.178 ELB improved by 0.123539 iteration 57 Updating parameters of variational distributions... Calculating ELB.. ELB=-393.075 ELB improved by 0.103036 iteration 58 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.993 ELB improved by 0.0817512 iteration 59 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.931 ELB improved by 0.0623225 iteration 60 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.884 ELB improved by 0.0468346 iteration 61 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.849 ELB improved by 0.0354935 iteration 62 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.821 ELB improved by 0.0274832 iteration 63 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.799 ELB improved by 0.021865 iteration 64 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.781 ELB improved by 0.0178962 iteration 65 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.766 ELB improved by 0.0150476 iteration 66 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.753 ELB improved by 0.0129546 iteration 67 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.742 ELB improved by 0.0113718 iteration 68 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.732 ELB improved by 0.0101368 iteration 69 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.723 ELB improved by 0.00914385 ELB converged [ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ] > > proc.time() user system elapsed 4.717 0.462 5.918
graper.Rcheck/graper-Ex.timings
name | user | system | elapsed | |
coef.graper | 0.086 | 0.042 | 0.155 | |
getPIPs | 0.078 | 0.037 | 0.135 | |
graper | 0.130 | 0.055 | 0.221 | |
makeExampleData | 0.020 | 0.002 | 0.027 | |
makeExampleDataWithUnequalGroups | 0.046 | 0.005 | 0.060 | |
plotELBO | 0.419 | 0.044 | 0.546 | |
plotGroupPenalties | 1.760 | 0.069 | 2.156 | |
plotPosterior | 1.252 | 0.047 | 1.502 | |
predict.graper | 3.184 | 0.204 | 3.953 | |
print.graper | 0.077 | 0.044 | 0.193 | |