Britta Velten
| Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 82b0592 |
| git_last_commit_date: 2025-06-24 03:15:40 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-27 12:06 -0400 (Sat, 27 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4832 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4620 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4565 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 913/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.25.2 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | 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: 1.25.2 |
| 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_1.25.2.tar.gz |
| StartedAt: 2025-09-26 19:43:45 -0400 (Fri, 26 Sep 2025) |
| EndedAt: 2025-09-26 19:44:15 -0400 (Fri, 26 Sep 2025) |
| EllapsedTime: 29.3 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_1.25.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.25.2’
* 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-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.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-3.22-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 ‘1.25.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.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 (2025-09-10 r88807) -- "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=-883.143
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-615.214
ELB improved by 267.929
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-556.03
ELB improved by 59.1846
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.418
ELB improved by 51.612
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.617
ELB improved by 28.8003
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.741
ELB improved by 10.876
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.62
ELB improved by 5.12194
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.83
ELB improved by 3.78948
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.206
ELB improved by 3.62428
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.323
ELB improved by 3.88238
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.063
ELB improved by 4.25993
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.628
ELB improved by 4.43551
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.532
ELB improved by 4.09639
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.282
ELB improved by 3.24935
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.999
ELB improved by 2.28275
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.462
ELB improved by 1.53757
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.399
ELB improved by 1.06261
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.619
ELB improved by 0.779938
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.002
ELB improved by 0.617475
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.476
ELB improved by 0.525733
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.002
ELB improved by 0.474066
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.556
ELB improved by 0.44567
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.124
ELB improved by 0.432452
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.692
ELB improved by 0.431819
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.248
ELB improved by 0.444629
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.777
ELB improved by 0.470511
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.28
ELB improved by 0.496916
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.781
ELB improved by 0.499072
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.31
ELB improved by 0.471168
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.879
ELB improved by 0.430344
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.491
ELB improved by 0.388002
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.144
ELB improved by 0.347143
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.835
ELB improved by 0.308914
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.561
ELB improved by 0.274101
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.318
ELB improved by 0.243068
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.102
ELB improved by 0.21581
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.91
ELB improved by 0.192084
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.739
ELB improved by 0.171542
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.585
ELB improved by 0.1538
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.447
ELB improved by 0.138488
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.321
ELB improved by 0.125269
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.207
ELB improved by 0.113845
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.103
ELB improved by 0.103962
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.008
ELB improved by 0.095405
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.92
ELB improved by 0.0879981
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.838
ELB improved by 0.0815977
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.762
ELB improved by 0.0760917
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.691
ELB improved by 0.0713982
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.624
ELB improved by 0.067467
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.559
ELB improved by 0.064286
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.497
ELB improved by 0.0618944
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.437
ELB improved by 0.0604126
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.377
ELB improved by 0.060103
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.315
ELB improved by 0.0615036
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.25
ELB improved by 0.0657293
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.174
ELB improved by 0.0751742
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.079
ELB improved by 0.0950803
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.943
ELB improved by 0.136037
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.732
ELB improved by 0.211203
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.425
ELB improved by 0.306647
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.051
ELB improved by 0.374366
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.583
ELB improved by 0.468274
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.906
ELB improved by 0.676837
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.073
ELB improved by 0.833217
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.327
ELB improved by 0.746096
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.819
ELB improved by 0.508047
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.48
ELB improved by 0.338577
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.215
ELB improved by 0.264933
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.966
ELB improved by 0.248861
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.707
ELB improved by 0.259138
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.445
ELB improved by 0.26161
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.213
ELB improved by 0.232581
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.03
ELB improved by 0.182421
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.896
ELB improved by 0.13452
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.798
ELB improved by 0.0982733
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.725
ELB improved by 0.0727501
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.67
ELB improved by 0.0550023
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.627
ELB improved by 0.0425352
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.594
ELB improved by 0.0335733
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.567
ELB improved by 0.0269425
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.545
ELB improved by 0.0219077
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.527
ELB improved by 0.0180227
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.512
ELB improved by 0.015011
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.499
ELB improved by 0.0126842
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.488
ELB improved by 0.0108969
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.479
ELB improved by 0.00952831
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-836.981
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-590.896
ELB improved by 246.085
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.146
ELB improved by 62.7501
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.715
ELB improved by 51.4305
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.182
ELB improved by 26.5331
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.736
ELB improved by 9.44615
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.218
ELB improved by 4.51788
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.953
ELB improved by 3.26489
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.946
ELB improved by 3.00723
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.796
ELB improved by 3.1499
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.262
ELB improved by 3.53391
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.208
ELB improved by 4.05467
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.738
ELB improved by 4.46933
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.325
ELB improved by 4.41284
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.561
ELB improved by 3.7648
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.702
ELB improved by 2.8584
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.599
ELB improved by 2.1031
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.965
ELB improved by 1.63423
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.563
ELB improved by 1.40192
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.218
ELB improved by 1.34502
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.876
ELB improved by 1.34224
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.747
ELB improved by 1.12866
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.872
ELB improved by 0.874861
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.131
ELB improved by 0.740673
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.478
ELB improved by 0.653437
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.893
ELB improved by 0.585248
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.362
ELB improved by 0.530923
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.874
ELB improved by 0.488161
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.419
ELB improved by 0.454979
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.989
ELB improved by 0.429709
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.578
ELB improved by 0.411119
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.18
ELB improved by 0.398413
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.789
ELB improved by 0.390979
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.401
ELB improved by 0.387631
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.016
ELB improved by 0.385284
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.637
ELB improved by 0.378603
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.273
ELB improved by 0.363528
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.931
ELB improved by 0.342818
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.604
ELB improved by 0.326676
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.272
ELB improved by 0.331759
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.883
ELB improved by 0.389494
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.338
ELB improved by 0.544463
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.619
ELB improved by 0.718908
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.884
ELB improved by 0.735417
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.205
ELB improved by 0.678662
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.692
ELB improved by 0.513732
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.384
ELB improved by 0.307341
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.205
ELB improved by 0.178757
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.091
ELB improved by 0.114298
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.011
ELB improved by 0.0805129
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.95
ELB improved by 0.060896
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.901
ELB improved by 0.048481
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.861
ELB improved by 0.0401205
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.827
ELB improved by 0.0342227
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.797
ELB improved by 0.0299021
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.77
ELB improved by 0.0266339
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.746
ELB improved by 0.0240951
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.724
ELB improved by 0.022081
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.704
ELB improved by 0.0204587
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.685
ELB improved by 0.0191387
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.667
ELB improved by 0.0180569
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.649
ELB improved by 0.017164
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.633
ELB improved by 0.0164175
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.617
ELB improved by 0.0157775
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.602
ELB improved by 0.0152042
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.587
ELB improved by 0.0146583
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.573
ELB improved by 0.0141035
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.56
ELB improved by 0.0135106
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.547
ELB improved by 0.0128625
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.535
ELB improved by 0.0121565
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.523
ELB improved by 0.0114042
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.513
ELB improved by 0.0106278
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.503
ELB improved by 0.00985346
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-889.895
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.423
ELB improved by 325.472
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-503.833
ELB improved by 60.5906
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.238
ELB improved by 31.5949
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.763
ELB improved by 12.4755
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.323
ELB improved by 5.43941
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.728
ELB improved by 3.59481
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.511
ELB improved by 3.21679
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.149
ELB improved by 3.36214
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.416
ELB improved by 3.73319
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.321
ELB improved by 4.09529
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.182
ELB improved by 4.13896
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.517
ELB improved by 3.66456
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.644
ELB improved by 2.87365
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.489
ELB improved by 2.15439
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.808
ELB improved by 1.68095
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.379
ELB improved by 1.42935
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.058
ELB improved by 1.32143
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.782
ELB improved by 1.27605
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.549
ELB improved by 1.23232
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.39
ELB improved by 1.15908
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.331
ELB improved by 1.05898
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.379
ELB improved by 0.952559
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.526
ELB improved by 0.852137
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.766
ELB improved by 0.760647
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.088
ELB improved by 0.67793
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.484
ELB improved by 0.603376
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.948
ELB improved by 0.536404
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.472
ELB improved by 0.476479
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.049
ELB improved by 0.423102
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.673
ELB improved by 0.375812
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.339
ELB improved by 0.334165
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.041
ELB improved by 0.297715
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.775
ELB improved by 0.266001
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.536
ELB improved by 0.238548
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.321
ELB improved by 0.214876
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.127
ELB improved by 0.194521
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.95
ELB improved by 0.177044
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.788
ELB improved by 0.162044
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.639
ELB improved by 0.149163
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.501
ELB improved by 0.138087
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.372
ELB improved by 0.128551
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.252
ELB improved by 0.120337
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.138
ELB improved by 0.113289
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.031
ELB improved by 0.107321
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.929
ELB improved by 0.102457
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.83
ELB improved by 0.0988982
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.733
ELB improved by 0.0971657
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.634
ELB improved by 0.098406
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.529
ELB improved by 0.104985
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.408
ELB improved by 0.121333
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.255
ELB improved by 0.1532
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.057
ELB improved by 0.197713
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.832
ELB improved by 0.224473
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.629
ELB improved by 0.20313
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.473
ELB improved by 0.155887
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.36
ELB improved by 0.113428
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.278
ELB improved by 0.0824459
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.217
ELB improved by 0.0606503
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.172
ELB improved by 0.045356
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.137
ELB improved by 0.0346063
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.11
ELB improved by 0.0270225
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.088
ELB improved by 0.0216311
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.071
ELB improved by 0.0177498
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.056
ELB improved by 0.0149064
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.043
ELB improved by 0.0127785
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.032
ELB improved by 0.0111483
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.022
ELB improved by 0.00986944
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-879.816
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.741
ELB improved by 304.075
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.702
ELB improved by 62.0389
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.453
ELB improved by 44.249
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.023
ELB improved by 21.4303
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.386
ELB improved by 8.6368
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.007
ELB improved by 4.3785
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.113
ELB improved by 2.89419
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.809
ELB improved by 2.30421
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.675
ELB improved by 2.13379
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.476
ELB improved by 2.19918
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.078
ELB improved by 2.39854
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.42
ELB improved by 2.65771
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.527
ELB improved by 2.89248
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.532
ELB improved by 2.99506
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.656
ELB improved by 2.87669
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.112
ELB improved by 2.54386
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.015
ELB improved by 2.09671
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.394
ELB improved by 1.62099
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.226
ELB improved by 1.16779
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.423
ELB improved by 0.802881
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.872
ELB improved by 0.55134
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.48
ELB improved by 0.391802
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.186
ELB improved by 0.294049
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.952
ELB improved by 0.234687
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.753
ELB improved by 0.198471
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.577
ELB improved by 0.176277
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.414
ELB improved by 0.162965
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.258
ELB improved by 0.155801
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.105
ELB improved by 0.153418
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.949
ELB improved by 0.155205
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.788
ELB improved by 0.160962
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.618
ELB improved by 0.170728
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.433
ELB improved by 0.184678
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.23
ELB improved by 0.203034
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.004
ELB improved by 0.225937
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.751
ELB improved by 0.253281
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.466
ELB improved by 0.284514
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.148
ELB improved by 0.318484
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.794
ELB improved by 0.353472
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.407
ELB improved by 0.387493
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.988
ELB improved by 0.418829
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.541
ELB improved by 0.446542
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.071
ELB improved by 0.470733
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.578
ELB improved by 0.492535
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.064
ELB improved by 0.51401
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.526
ELB improved by 0.538164
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.957
ELB improved by 0.569341
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.342
ELB improved by 0.614616
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.656
ELB improved by 0.68566
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.87
ELB improved by 0.786247
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.017
ELB improved by 0.853089
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.227
ELB improved by 0.790482
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.556
ELB improved by 0.670371
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.95
ELB improved by 0.605727
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.341
ELB improved by 0.60953
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.745
ELB improved by 0.595901
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.269
ELB improved by 0.475716
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.941
ELB improved by 0.328436
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.708
ELB improved by 0.232394
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.526
ELB improved by 0.182044
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.37
ELB improved by 0.156361
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.232
ELB improved by 0.138185
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.117
ELB improved by 0.11495
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.032
ELB improved by 0.0853789
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.973
ELB improved by 0.0586328
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.932
ELB improved by 0.0407476
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.902
ELB improved by 0.0303999
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.877
ELB improved by 0.0243584
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.857
ELB improved by 0.0205012
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.839
ELB improved by 0.0177881
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.823
ELB improved by 0.0157339
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.809
ELB improved by 0.0140992
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.797
ELB improved by 0.0127544
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.785
ELB improved by 0.0116225
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.774
ELB improved by 0.010654
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.764
ELB improved by 0.00981493
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.072 0.098 1.179
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.028 | 0.007 | 0.035 | |
| getPIPs | 0.027 | 0.006 | 0.033 | |
| graper | 0.051 | 0.010 | 0.063 | |
| makeExampleData | 0.004 | 0.000 | 0.004 | |
| makeExampleDataWithUnequalGroups | 0.005 | 0.000 | 0.005 | |
| plotELBO | 0.123 | 0.009 | 0.152 | |
| plotGroupPenalties | 0.440 | 0.012 | 0.459 | |
| plotPosterior | 0.220 | 0.013 | 0.236 | |
| predict.graper | 1.025 | 0.036 | 1.091 | |
| print.graper | 0.027 | 0.006 | 0.033 | |