Britta Velten
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_21 |
| git_last_commit: fb5f237 |
| git_last_commit_date: 2025-06-24 03:18:49 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
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 | |