Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 915/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
graper 1.24.2 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | 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: 1.24.2 |
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_1.24.2.tar.gz |
StartedAt: 2025-10-14 23:47:15 -0400 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 23:48:33 -0400 (Tue, 14 Oct 2025) |
EllapsedTime: 78.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: graper.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.24.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘graper/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘graper’ version ‘1.24.2’ * 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 ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-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/4.5-arm64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.24.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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 clang++ -arch arm64 -std=gnu++17 -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-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 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=-912.76 ELB improved by inf iteration 2 Updating parameters of variational distributions... Calculating ELB.. ELB=-584.579 ELB improved by 328.181 iteration 3 Updating parameters of variational distributions... Calculating ELB.. ELB=-527.528 ELB improved by 57.0502 iteration 4 Updating parameters of variational distributions... Calculating ELB.. ELB=-495.074 ELB improved by 32.4546 iteration 5 Updating parameters of variational distributions... Calculating ELB.. ELB=-480.525 ELB improved by 14.5492 iteration 6 Updating parameters of variational distributions... Calculating ELB.. ELB=-474.006 ELB improved by 6.51858 iteration 7 Updating parameters of variational distributions... Calculating ELB.. ELB=-469.605 ELB improved by 4.40155 iteration 8 Updating parameters of variational distributions... Calculating ELB.. ELB=-465.645 ELB improved by 3.95955 iteration 9 Updating parameters of variational distributions... Calculating ELB.. ELB=-461.688 ELB improved by 3.9566 iteration 10 Updating parameters of variational distributions... Calculating ELB.. ELB=-457.738 ELB improved by 3.94997 iteration 11 Updating parameters of variational distributions... Calculating ELB.. ELB=-454.084 ELB improved by 3.65485 iteration 12 Updating parameters of variational distributions... Calculating ELB.. ELB=-451.056 ELB improved by 3.02802 iteration 13 Updating parameters of variational distributions... Calculating ELB.. ELB=-448.784 ELB improved by 2.27111 iteration 14 Updating parameters of variational distributions... Calculating ELB.. ELB=-447.166 ELB improved by 1.61853 iteration 15 Updating parameters of variational distributions... Calculating ELB.. ELB=-446.012 ELB improved by 1.15366 iteration 16 Updating parameters of variational distributions... Calculating ELB.. ELB=-445.172 ELB improved by 0.839768 iteration 17 Updating parameters of variational distributions... Calculating ELB.. ELB=-444.544 ELB improved by 0.628036 iteration 18 Updating parameters of variational distributions... Calculating ELB.. ELB=-444.059 ELB improved by 0.485296 iteration 19 Updating parameters of variational distributions... Calculating ELB.. ELB=-443.672 ELB improved by 0.386996 iteration 20 Updating parameters of variational distributions... Calculating ELB.. ELB=-443.355 ELB improved by 0.31678 iteration 21 Updating parameters of variational distributions... Calculating ELB.. ELB=-443.09 ELB improved by 0.264892 iteration 22 Updating parameters of variational distributions... Calculating ELB.. ELB=-442.865 ELB improved by 0.22539 iteration 23 Updating parameters of variational distributions... Calculating ELB.. ELB=-442.671 ELB improved by 0.194476 iteration 24 Updating parameters of variational distributions... Calculating ELB.. ELB=-442.501 ELB improved by 0.169685 iteration 25 Updating parameters of variational distributions... Calculating ELB.. ELB=-442.351 ELB improved by 0.14941 iteration 26 Updating parameters of variational distributions... Calculating ELB.. ELB=-442.219 ELB improved by 0.13258 iteration 27 Updating parameters of variational distributions... Calculating ELB.. ELB=-442.1 ELB improved by 0.118448 iteration 28 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.994 ELB improved by 0.106468 iteration 29 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.898 ELB improved by 0.0962304 iteration 30 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.81 ELB improved by 0.0874184 iteration 31 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.731 ELB improved by 0.0797828 iteration 32 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.657 ELB improved by 0.0731257 iteration 33 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.59 ELB improved by 0.0672887 iteration 34 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.528 ELB improved by 0.0621437 iteration 35 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.47 ELB improved by 0.0575867 iteration 36 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.417 ELB improved by 0.053532 iteration 37 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.367 ELB improved by 0.0499091 iteration 38 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.32 ELB improved by 0.046659 iteration 39 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.277 ELB improved by 0.0437326 iteration 40 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.236 ELB improved by 0.0410881 iteration 41 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.197 ELB improved by 0.0386904 iteration 42 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.16 ELB improved by 0.0365092 iteration 43 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.126 ELB improved by 0.0345189 iteration 44 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.093 ELB improved by 0.0326971 iteration 45 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.062 ELB improved by 0.0310247 iteration 46 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.033 ELB improved by 0.0294849 iteration 47 Updating parameters of variational distributions... Calculating ELB.. ELB=-441.005 ELB improved by 0.0280634 iteration 48 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.978 ELB improved by 0.0267473 iteration 49 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.952 ELB improved by 0.0255257 iteration 50 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.928 ELB improved by 0.0243887 iteration 51 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.905 ELB improved by 0.0233279 iteration 52 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.882 ELB improved by 0.0223358 iteration 53 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.861 ELB improved by 0.0214058 iteration 54 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.84 ELB improved by 0.020532 iteration 55 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.821 ELB improved by 0.0197094 iteration 56 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.802 ELB improved by 0.0189333 iteration 57 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.783 ELB improved by 0.0181998 iteration 58 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.766 ELB improved by 0.0175055 iteration 59 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.749 ELB improved by 0.0168471 iteration 60 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.733 ELB improved by 0.0162219 iteration 61 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.717 ELB improved by 0.0156276 iteration 62 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.702 ELB improved by 0.0150619 iteration 63 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.688 ELB improved by 0.0145231 iteration 64 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.674 ELB improved by 0.0140094 iteration 65 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.66 ELB improved by 0.0135193 iteration 66 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.647 ELB improved by 0.0130515 iteration 67 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.634 ELB improved by 0.0126049 iteration 68 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.622 ELB improved by 0.0121783 iteration 69 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.61 ELB improved by 0.0117708 iteration 70 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.599 ELB improved by 0.0113816 iteration 71 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.588 ELB improved by 0.0110099 iteration 72 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.577 ELB improved by 0.0106549 iteration 73 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.567 ELB improved by 0.010316 iteration 74 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.557 ELB improved by 0.00999261 ELB converged iteration 1 Updating parameters of variational distributions... Calculating ELB.. ELB=-856.706 ELB improved by inf iteration 2 Updating parameters of variational distributions... Calculating ELB.. ELB=-579.743 ELB improved by 276.963 iteration 3 Updating parameters of variational distributions... Calculating ELB.. ELB=-516.969 ELB improved by 62.7749 iteration 4 Updating parameters of variational distributions... Calculating ELB.. ELB=-473.59 ELB improved by 43.3784 iteration 5 Updating parameters of variational distributions... Calculating ELB.. ELB=-454.107 ELB improved by 19.4832 iteration 6 Updating parameters of variational distributions... Calculating ELB.. ELB=-446.268 ELB improved by 7.83888 iteration 7 Updating parameters of variational distributions... Calculating ELB.. ELB=-442.012 ELB improved by 4.25596 iteration 8 Updating parameters of variational distributions... Calculating ELB.. ELB=-438.856 ELB improved by 3.15632 iteration 9 Updating parameters of variational distributions... Calculating ELB.. ELB=-436.076 ELB improved by 2.77952 iteration 10 Updating parameters of variational distributions... Calculating ELB.. ELB=-433.381 ELB improved by 2.69508 iteration 11 Updating parameters of variational distributions... Calculating ELB.. ELB=-430.617 ELB improved by 2.7643 iteration 12 Updating parameters of variational distributions... Calculating ELB.. ELB=-427.706 ELB improved by 2.91091 iteration 13 Updating parameters of variational distributions... Calculating ELB.. ELB=-424.663 ELB improved by 3.04346 iteration 14 Updating parameters of variational distributions... Calculating ELB.. ELB=-421.616 ELB improved by 3.04609 iteration 15 Updating parameters of variational distributions... Calculating ELB.. ELB=-418.778 ELB improved by 2.83871 iteration 16 Updating parameters of variational distributions... Calculating ELB.. ELB=-416.335 ELB improved by 2.44233 iteration 17 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.364 ELB improved by 1.97126 iteration 18 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.805 ELB improved by 1.55898 iteration 19 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.534 ELB improved by 1.27123 iteration 20 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.439 ELB improved by 1.09487 iteration 21 Updating parameters of variational distributions... Calculating ELB.. ELB=-409.438 ELB improved by 1.00085 iteration 22 Updating parameters of variational distributions... Calculating ELB.. ELB=-408.469 ELB improved by 0.969005 iteration 23 Updating parameters of variational distributions... Calculating ELB.. ELB=-407.49 ELB improved by 0.978758 iteration 24 Updating parameters of variational distributions... Calculating ELB.. ELB=-406.476 ELB improved by 1.01407 iteration 25 Updating parameters of variational distributions... Calculating ELB.. ELB=-405.408 ELB improved by 1.06867 iteration 26 Updating parameters of variational distributions... Calculating ELB.. ELB=-404.264 ELB improved by 1.14356 iteration 27 Updating parameters of variational distributions... Calculating ELB.. ELB=-403.026 ELB improved by 1.23828 iteration 28 Updating parameters of variational distributions... Calculating ELB.. ELB=-401.685 ELB improved by 1.3412 iteration 29 Updating parameters of variational distributions... Calculating ELB.. ELB=-400.248 ELB improved by 1.43637 iteration 30 Updating parameters of variational distributions... Calculating ELB.. ELB=-398.732 ELB improved by 1.51674 iteration 31 Updating parameters of variational distributions... Calculating ELB.. ELB=-397.156 ELB improved by 1.57515 iteration 32 Updating parameters of variational distributions... Calculating ELB.. ELB=-395.56 ELB improved by 1.59599 iteration 33 Updating parameters of variational distributions... Calculating ELB.. ELB=-394.002 ELB improved by 1.55882 iteration 34 Updating parameters of variational distributions... Calculating ELB.. ELB=-392.555 ELB improved by 1.44681 iteration 35 Updating parameters of variational distributions... Calculating ELB.. ELB=-391.289 ELB improved by 1.26618 iteration 36 Updating parameters of variational distributions... Calculating ELB.. ELB=-390.237 ELB improved by 1.05167 iteration 37 Updating parameters of variational distributions... Calculating ELB.. ELB=-389.399 ELB improved by 0.83778 iteration 38 Updating parameters of variational distributions... Calculating ELB.. ELB=-388.755 ELB improved by 0.644156 iteration 39 Updating parameters of variational distributions... Calculating ELB.. ELB=-388.262 ELB improved by 0.49266 iteration 40 Updating parameters of variational distributions... Calculating ELB.. ELB=-387.867 ELB improved by 0.395707 iteration 41 Updating parameters of variational distributions... Calculating ELB.. ELB=-387.523 ELB improved by 0.343487 iteration 42 Updating parameters of variational distributions... Calculating ELB.. ELB=-387.21 ELB improved by 0.313467 iteration 43 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.936 ELB improved by 0.274094 iteration 44 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.725 ELB improved by 0.210684 iteration 45 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.577 ELB improved by 0.147518 iteration 46 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.472 ELB improved by 0.105283 iteration 47 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.391 ELB improved by 0.0813045 iteration 48 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.324 ELB improved by 0.0670081 iteration 49 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.267 ELB improved by 0.0567373 iteration 50 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.219 ELB improved by 0.0479215 iteration 51 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.179 ELB improved by 0.0398442 iteration 52 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.147 ELB improved by 0.0326151 iteration 53 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.12 ELB improved by 0.0264812 iteration 54 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.099 ELB improved by 0.0215274 iteration 55 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.081 ELB improved by 0.0176635 iteration 56 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.066 ELB improved by 0.0147091 iteration 57 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.054 ELB improved by 0.0124667 iteration 58 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.043 ELB improved by 0.0107593 iteration 59 Updating parameters of variational distributions... Calculating ELB.. ELB=-386.034 ELB improved by 0.00944387 ELB converged iteration 1 Updating parameters of variational distributions... Calculating ELB.. ELB=-864.38 ELB improved by inf iteration 2 Updating parameters of variational distributions... Calculating ELB.. ELB=-599.685 ELB improved by 264.695 iteration 3 Updating parameters of variational distributions... Calculating ELB.. ELB=-540.681 ELB improved by 59.0039 iteration 4 Updating parameters of variational distributions... Calculating ELB.. ELB=-491.585 ELB improved by 49.0967 iteration 5 Updating parameters of variational distributions... Calculating ELB.. ELB=-464 ELB improved by 27.5843 iteration 6 Updating parameters of variational distributions... Calculating ELB.. ELB=-452.826 ELB improved by 11.1747 iteration 7 Updating parameters of variational distributions... Calculating ELB.. ELB=-447.977 ELB improved by 4.84819 iteration 8 Updating parameters of variational distributions... Calculating ELB.. ELB=-444.939 ELB improved by 3.03844 iteration 9 Updating parameters of variational distributions... Calculating ELB.. ELB=-442.509 ELB improved by 2.43036 iteration 10 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.332 ELB improved by 2.17632 iteration 11 Updating parameters of variational distributions... Calculating ELB.. ELB=-438.264 ELB improved by 2.06802 iteration 12 Updating parameters of variational distributions... Calculating ELB.. ELB=-436.243 ELB improved by 2.02091 iteration 13 Updating parameters of variational distributions... Calculating ELB.. ELB=-434.25 ELB improved by 1.99375 iteration 14 Updating parameters of variational distributions... Calculating ELB.. ELB=-432.292 ELB improved by 1.95743 iteration 15 Updating parameters of variational distributions... Calculating ELB.. ELB=-430.408 ELB improved by 1.88405 iteration 16 Updating parameters of variational distributions... Calculating ELB.. ELB=-428.655 ELB improved by 1.75322 iteration 17 Updating parameters of variational distributions... Calculating ELB.. ELB=-427.09 ELB improved by 1.56526 iteration 18 Updating parameters of variational distributions... Calculating ELB.. ELB=-425.746 ELB improved by 1.34358 iteration 19 Updating parameters of variational distributions... Calculating ELB.. ELB=-424.625 ELB improved by 1.12149 iteration 20 Updating parameters of variational distributions... Calculating ELB.. ELB=-423.695 ELB improved by 0.929747 iteration 21 Updating parameters of variational distributions... Calculating ELB.. ELB=-422.906 ELB improved by 0.788812 iteration 22 Updating parameters of variational distributions... Calculating ELB.. ELB=-422.204 ELB improved by 0.702055 iteration 23 Updating parameters of variational distributions... Calculating ELB.. ELB=-421.549 ELB improved by 0.654927 iteration 24 Updating parameters of variational distributions... Calculating ELB.. ELB=-420.926 ELB improved by 0.622879 iteration 25 Updating parameters of variational distributions... Calculating ELB.. ELB=-420.335 ELB improved by 0.590822 iteration 26 Updating parameters of variational distributions... Calculating ELB.. ELB=-419.771 ELB improved by 0.564696 iteration 27 Updating parameters of variational distributions... Calculating ELB.. ELB=-419.216 ELB improved by 0.554861 iteration 28 Updating parameters of variational distributions... Calculating ELB.. ELB=-418.654 ELB improved by 0.561758 iteration 29 Updating parameters of variational distributions... Calculating ELB.. ELB=-418.074 ELB improved by 0.579945 iteration 30 Updating parameters of variational distributions... Calculating ELB.. ELB=-417.47 ELB improved by 0.604424 iteration 31 Updating parameters of variational distributions... Calculating ELB.. ELB=-416.837 ELB improved by 0.632618 iteration 32 Updating parameters of variational distributions... Calculating ELB.. ELB=-416.173 ELB improved by 0.664334 iteration 33 Updating parameters of variational distributions... Calculating ELB.. ELB=-415.471 ELB improved by 0.701508 iteration 34 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.723 ELB improved by 0.747638 iteration 35 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.917 ELB improved by 0.806156 iteration 36 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.039 ELB improved by 0.878316 iteration 37 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.077 ELB improved by 0.962075 iteration 38 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.026 ELB improved by 1.05108 iteration 39 Updating parameters of variational distributions... Calculating ELB.. ELB=-409.893 ELB improved by 1.13263 iteration 40 Updating parameters of variational distributions... Calculating ELB.. ELB=-408.707 ELB improved by 1.18647 iteration 41 Updating parameters of variational distributions... Calculating ELB.. ELB=-407.52 ELB improved by 1.18663 iteration 42 Updating parameters of variational distributions... Calculating ELB.. ELB=-406.41 ELB improved by 1.10987 iteration 43 Updating parameters of variational distributions... Calculating ELB.. ELB=-405.457 ELB improved by 0.953169 iteration 44 Updating parameters of variational distributions... Calculating ELB.. ELB=-404.71 ELB improved by 0.746886 iteration 45 Updating parameters of variational distributions... Calculating ELB.. ELB=-404.169 ELB improved by 0.541255 iteration 46 Updating parameters of variational distributions... Calculating ELB.. ELB=-403.795 ELB improved by 0.374112 iteration 47 Updating parameters of variational distributions... Calculating ELB.. ELB=-403.539 ELB improved by 0.255641 iteration 48 Updating parameters of variational distributions... Calculating ELB.. ELB=-403.362 ELB improved by 0.177662 iteration 49 Updating parameters of variational distributions... Calculating ELB.. ELB=-403.234 ELB improved by 0.127523 iteration 50 Updating parameters of variational distributions... Calculating ELB.. ELB=-403.139 ELB improved by 0.0949686 iteration 51 Updating parameters of variational distributions... Calculating ELB.. ELB=-403.066 ELB improved by 0.0732619 iteration 52 Updating parameters of variational distributions... Calculating ELB.. ELB=-403.007 ELB improved by 0.0583106 iteration 53 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.96 ELB improved by 0.0476666 iteration 54 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.92 ELB improved by 0.0398461 iteration 55 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.886 ELB improved by 0.0339288 iteration 56 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.857 ELB improved by 0.0293303 iteration 57 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.831 ELB improved by 0.0256706 iteration 58 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.808 ELB improved by 0.0226975 iteration 59 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.788 ELB improved by 0.0202395 iteration 60 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.77 ELB improved by 0.0181778 iteration 61 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.754 ELB improved by 0.0164276 iteration 62 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.739 ELB improved by 0.0149273 iteration 63 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.725 ELB improved by 0.0136307 iteration 64 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.712 ELB improved by 0.0125026 iteration 65 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.701 ELB improved by 0.0115156 iteration 66 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.69 ELB improved by 0.0106476 iteration 67 Updating parameters of variational distributions... Calculating ELB.. ELB=-402.68 ELB improved by 0.00988113 ELB converged iteration 1 Updating parameters of variational distributions... Calculating ELB.. ELB=-844.068 ELB improved by inf iteration 2 Updating parameters of variational distributions... Calculating ELB.. ELB=-567.467 ELB improved by 276.602 iteration 3 Updating parameters of variational distributions... Calculating ELB.. ELB=-509.24 ELB improved by 58.2266 iteration 4 Updating parameters of variational distributions... Calculating ELB.. ELB=-467.67 ELB improved by 41.5703 iteration 5 Updating parameters of variational distributions... Calculating ELB.. ELB=-449.677 ELB improved by 17.9924 iteration 6 Updating parameters of variational distributions... Calculating ELB.. ELB=-443.372 ELB improved by 6.30588 iteration 7 Updating parameters of variational distributions... Calculating ELB.. ELB=-440.212 ELB improved by 3.15928 iteration 8 Updating parameters of variational distributions... Calculating ELB.. ELB=-437.999 ELB improved by 2.2134 iteration 9 Updating parameters of variational distributions... Calculating ELB.. ELB=-436.127 ELB improved by 1.87156 iteration 10 Updating parameters of variational distributions... Calculating ELB.. ELB=-434.375 ELB improved by 1.75192 iteration 11 Updating parameters of variational distributions... Calculating ELB.. ELB=-432.639 ELB improved by 1.73633 iteration 12 Updating parameters of variational distributions... Calculating ELB.. ELB=-430.859 ELB improved by 1.7801 iteration 13 Updating parameters of variational distributions... Calculating ELB.. ELB=-428.997 ELB improved by 1.86188 iteration 14 Updating parameters of variational distributions... Calculating ELB.. ELB=-427.036 ELB improved by 1.96082 iteration 15 Updating parameters of variational distributions... Calculating ELB.. ELB=-424.99 ELB improved by 2.04659 iteration 16 Updating parameters of variational distributions... Calculating ELB.. ELB=-422.905 ELB improved by 2.08475 iteration 17 Updating parameters of variational distributions... Calculating ELB.. ELB=-420.846 ELB improved by 2.05863 iteration 18 Updating parameters of variational distributions... Calculating ELB.. ELB=-418.863 ELB improved by 1.98304 iteration 19 Updating parameters of variational distributions... Calculating ELB.. ELB=-417.005 ELB improved by 1.85826 iteration 20 Updating parameters of variational distributions... Calculating ELB.. ELB=-415.4 ELB improved by 1.60472 iteration 21 Updating parameters of variational distributions... Calculating ELB.. ELB=-414.19 ELB improved by 1.21023 iteration 22 Updating parameters of variational distributions... Calculating ELB.. ELB=-413.365 ELB improved by 0.825123 iteration 23 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.819 ELB improved by 0.545674 iteration 24 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.45 ELB improved by 0.369275 iteration 25 Updating parameters of variational distributions... Calculating ELB.. ELB=-412.187 ELB improved by 0.26346 iteration 26 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.987 ELB improved by 0.199806 iteration 27 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.827 ELB improved by 0.160179 iteration 28 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.692 ELB improved by 0.134273 iteration 29 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.576 ELB improved by 0.116402 iteration 30 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.472 ELB improved by 0.103399 iteration 31 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.379 ELB improved by 0.0934491 iteration 32 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.294 ELB improved by 0.0854851 iteration 33 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.215 ELB improved by 0.078859 iteration 34 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.141 ELB improved by 0.0731677 iteration 35 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.073 ELB improved by 0.0681543 iteration 36 Updating parameters of variational distributions... Calculating ELB.. ELB=-411.01 ELB improved by 0.0636515 iteration 37 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.95 ELB improved by 0.0595482 iteration 38 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.894 ELB improved by 0.055769 iteration 39 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.842 ELB improved by 0.0522624 iteration 40 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.793 ELB improved by 0.0489919 iteration 41 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.747 ELB improved by 0.0459317 iteration 42 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.704 ELB improved by 0.0430629 iteration 43 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.664 ELB improved by 0.0403712 iteration 44 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.626 ELB improved by 0.0378452 iteration 45 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.59 ELB improved by 0.0354757 iteration 46 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.557 ELB improved by 0.0332545 iteration 47 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.526 ELB improved by 0.0311741 iteration 48 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.497 ELB improved by 0.0292277 iteration 49 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.469 ELB improved by 0.0274084 iteration 50 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.444 ELB improved by 0.0257095 iteration 51 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.42 ELB improved by 0.0241244 iteration 52 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.397 ELB improved by 0.0226466 iteration 53 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.376 ELB improved by 0.0212698 iteration 54 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.356 ELB improved by 0.0199876 iteration 55 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.337 ELB improved by 0.0187939 iteration 56 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.319 ELB improved by 0.0176829 iteration 57 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.303 ELB improved by 0.0166488 iteration 58 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.287 ELB improved by 0.0156865 iteration 59 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.272 ELB improved by 0.0147906 iteration 60 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.258 ELB improved by 0.0139565 iteration 61 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.245 ELB improved by 0.0131796 iteration 62 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.232 ELB improved by 0.0124558 iteration 63 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.221 ELB improved by 0.0117811 iteration 64 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.21 ELB improved by 0.0111519 iteration 65 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.199 ELB improved by 0.0105648 iteration 66 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.189 ELB improved by 0.0100167 iteration 67 Updating parameters of variational distributions... Calculating ELB.. ELB=-410.179 ELB improved by 0.00950475 ELB converged [ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ] > > proc.time() user system elapsed 2.898 0.289 3.219
graper.Rcheck/graper-Ex.timings
name | user | system | elapsed | |
coef.graper | 0.082 | 0.018 | 0.101 | |
getPIPs | 0.078 | 0.014 | 0.093 | |
graper | 0.130 | 0.020 | 0.154 | |
makeExampleData | 0.012 | 0.001 | 0.014 | |
makeExampleDataWithUnequalGroups | 0.015 | 0.002 | 0.016 | |
plotELBO | 0.385 | 0.025 | 0.413 | |
plotGroupPenalties | 1.354 | 0.055 | 1.426 | |
plotPosterior | 0.711 | 0.040 | 0.762 | |
predict.graper | 2.982 | 0.081 | 3.097 | |
print.graper | 0.031 | 0.006 | 0.037 | |