Britta Velten
| Snapshot Date: 2026-03-15 13:40 -0400 (Sun, 15 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 95474d7 |
| git_last_commit_date: 2025-10-29 10:49:21 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-16 11:34 -0400 (Mon, 16 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4837 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4053 |
| 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 928/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | ERROR | |||||||||
| See other builds for graper in R Universe. | ||||||||||||||
|
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: 1.27.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz |
| StartedAt: 2026-03-15 18:33:58 -0400 (Sun, 15 Mar 2026) |
| EndedAt: 2026-03-15 18:34:24 -0400 (Sun, 15 Mar 2026) |
| EllapsedTime: 26.3 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_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-15 22:33:58 UTC
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
* used SDK: ‘MacOSX14.4.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 ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-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/4.6/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’ using SDK: ‘MacOSX14.4.sdk’ clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -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/4.6/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 Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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=-873.694
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.199
ELB improved by 295.496
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.448
ELB improved by 61.751
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.686
ELB improved by 42.7615
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.374
ELB improved by 18.3122
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.747
ELB improved by 7.62684
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.861
ELB improved by 4.88601
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.579
ELB improved by 4.28256
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.274
ELB improved by 4.30514
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.698
ELB improved by 4.5757
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.787
ELB improved by 4.91074
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.759
ELB improved by 5.0285
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.163
ELB improved by 4.59598
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.558
ELB improved by 3.60415
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.076
ELB improved by 2.48198
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.45
ELB improved by 1.62657
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.34
ELB improved by 1.1098
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.506
ELB improved by 0.83406
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.805
ELB improved by 0.701121
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.154
ELB improved by 0.650439
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.505
ELB improved by 0.649547
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.826
ELB improved by 0.679332
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.104
ELB improved by 0.72152
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.346
ELB improved by 0.758199
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.563
ELB improved by 0.782533
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.765
ELB improved by 0.797889
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.957
ELB improved by 0.808428
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.14
ELB improved by 0.816542
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.317
ELB improved by 0.823313
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.489
ELB improved by 0.828341
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.659
ELB improved by 0.829618
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.835
ELB improved by 0.823848
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.028
ELB improved by 0.806956
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.254
ELB improved by 0.774517
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.531
ELB improved by 0.722539
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.882
ELB improved by 0.649554
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.322
ELB improved by 0.559423
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.861
ELB improved by 0.461698
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.493
ELB improved by 0.36785
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.206
ELB improved by 0.286464
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.985
ELB improved by 0.22118
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.814
ELB improved by 0.171625
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.678
ELB improved by 0.135395
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.569
ELB improved by 0.109644
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.477
ELB improved by 0.091872
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.397
ELB improved by 0.0801082
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.324
ELB improved by 0.0727585
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.255
ELB improved by 0.0683437
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.19
ELB improved by 0.065298
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.128
ELB improved by 0.062035
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.071
ELB improved by 0.0573801
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.02
ELB improved by 0.0510778
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.976
ELB improved by 0.0438032
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.939
ELB improved by 0.036573
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.909
ELB improved by 0.0301332
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.884
ELB improved by 0.0247737
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.864
ELB improved by 0.0204645
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.847
ELB improved by 0.0170428
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.833
ELB improved by 0.0143267
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.82
ELB improved by 0.0121603
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.81
ELB improved by 0.0104209
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.801
ELB improved by 0.00901555
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-851.536
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.788
ELB improved by 279.749
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.317
ELB improved by 58.4701
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.178
ELB improved by 39.1395
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.456
ELB improved by 17.7219
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.94
ELB improved by 6.51557
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.587
ELB improved by 3.35305
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.075
ELB improved by 2.51222
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.854
ELB improved by 2.22117
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.739
ELB improved by 2.11507
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.674
ELB improved by 2.06442
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.67
ELB improved by 2.00459
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.773
ELB improved by 1.89724
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.045
ELB improved by 1.72785
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.537
ELB improved by 1.50774
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.275
ELB improved by 1.26165
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.265
ELB improved by 1.01062
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.494
ELB improved by 0.770322
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.933
ELB improved by 0.561679
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.53
ELB improved by 0.402632
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.237
ELB improved by 0.293185
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.016
ELB improved by 0.221189
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.842
ELB improved by 0.173709
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.701
ELB improved by 0.141456
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.582
ELB improved by 0.11866
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.48
ELB improved by 0.101889
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.391
ELB improved by 0.0891011
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.312
ELB improved by 0.0790493
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.241
ELB improved by 0.0709453
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.177
ELB improved by 0.0642725
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.118
ELB improved by 0.058681
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.064
ELB improved by 0.0539257
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.014
ELB improved by 0.0498301
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.968
ELB improved by 0.0462647
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.925
ELB improved by 0.0431318
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.884
ELB improved by 0.0403568
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.847
ELB improved by 0.0378819
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.811
ELB improved by 0.0356616
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.777
ELB improved by 0.0336595
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.745
ELB improved by 0.0318467
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.715
ELB improved by 0.0301992
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.687
ELB improved by 0.0286976
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.659
ELB improved by 0.0273256
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.633
ELB improved by 0.0260697
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.608
ELB improved by 0.0249183
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.584
ELB improved by 0.0238613
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.561
ELB improved by 0.0228903
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.539
ELB improved by 0.0219975
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.518
ELB improved by 0.0211764
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.498
ELB improved by 0.020421
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.478
ELB improved by 0.0197261
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.459
ELB improved by 0.0190867
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.441
ELB improved by 0.0184986
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.423
ELB improved by 0.0179579
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.405
ELB improved by 0.0174609
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.388
ELB improved by 0.0170045
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.372
ELB improved by 0.0165856
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.355
ELB improved by 0.0162014
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.34
ELB improved by 0.0158496
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.324
ELB improved by 0.0155278
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.309
ELB improved by 0.0152338
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.294
ELB improved by 0.0149658
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.279
ELB improved by 0.014722
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.265
ELB improved by 0.0145007
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.25
ELB improved by 0.0143003
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.236
ELB improved by 0.0141196
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.222
ELB improved by 0.0139572
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.208
ELB improved by 0.0138119
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.195
ELB improved by 0.0136826
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.181
ELB improved by 0.0135683
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.168
ELB improved by 0.0134679
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.154
ELB improved by 0.0133805
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.141
ELB improved by 0.0133054
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.128
ELB improved by 0.0132417
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.115
ELB improved by 0.0131885
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.101
ELB improved by 0.0131451
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.088
ELB improved by 0.0131109
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.075
ELB improved by 0.013085
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.062
ELB improved by 0.0130667
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.049
ELB improved by 0.0130554
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.036
ELB improved by 0.0130502
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.023
ELB improved by 0.0130506
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.01
ELB improved by 0.0130556
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.997
ELB improved by 0.0130646
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.984
ELB improved by 0.0130768
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.971
ELB improved by 0.0130913
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.958
ELB improved by 0.0131072
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.944
ELB improved by 0.0131237
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.931
ELB improved by 0.0131398
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.918
ELB improved by 0.0131546
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.905
ELB improved by 0.013167
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.892
ELB improved by 0.0131761
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.879
ELB improved by 0.0131808
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.865
ELB improved by 0.01318
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.852
ELB improved by 0.0131726
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.839
ELB improved by 0.0131577
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.826
ELB improved by 0.0131341
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.813
ELB improved by 0.0131008
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.8
ELB improved by 0.0130569
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.787
ELB improved by 0.0130015
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.774
ELB improved by 0.0129337
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.761
ELB improved by 0.0128529
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.748
ELB improved by 0.0127584
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.736
ELB improved by 0.0126498
iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.723
ELB improved by 0.0125268
iteration 106
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.711
ELB improved by 0.0123892
iteration 107
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.698
ELB improved by 0.012237
iteration 108
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.686
ELB improved by 0.0120704
iteration 109
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.675
ELB improved by 0.0118898
iteration 110
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.663
ELB improved by 0.0116956
iteration 111
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.651
ELB improved by 0.0114886
iteration 112
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.64
ELB improved by 0.0112696
iteration 113
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.629
ELB improved by 0.0110396
iteration 114
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.618
ELB improved by 0.0107996
iteration 115
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.608
ELB improved by 0.0105509
iteration 116
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.597
ELB improved by 0.0102947
iteration 117
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.587
ELB improved by 0.0100323
iteration 118
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.578
ELB improved by 0.00976509
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-825.056
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.603
ELB improved by 251.452
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.292
ELB improved by 62.311
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.552
ELB improved by 47.7401
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.236
ELB improved by 23.3167
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.16
ELB improved by 10.076
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.794
ELB improved by 6.36507
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.878
ELB improved by 5.91693
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.401
ELB improved by 6.47628
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.437
ELB improved by 6.96404
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.966
ELB improved by 6.47087
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.02
ELB improved by 4.94634
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.72
ELB improved by 3.30051
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.532
ELB improved by 2.18747
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.939
ELB improved by 1.59319
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.637
ELB improved by 1.30154
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.48
ELB improved by 1.15735
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.399
ELB improved by 1.08114
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.361
ELB improved by 1.03793
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.347
ELB improved by 1.01426
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.342
ELB improved by 1.00515
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.334
ELB improved by 1.00734
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.318
ELB improved by 1.01596
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.295
ELB improved by 1.02331
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.276
ELB improved by 1.0193
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.282
ELB improved by 0.993478
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.344
ELB improved by 0.938365
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.491
ELB improved by 0.852617
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.749
ELB improved by 0.742162
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.13
ELB improved by 0.61881
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.634
ELB improved by 0.496583
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.247
ELB improved by 0.387052
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.95
ELB improved by 0.296474
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.724
ELB improved by 0.225851
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.551
ELB improved by 0.172789
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.418
ELB improved by 0.13362
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.313
ELB improved by 0.104796
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.23
ELB improved by 0.0834596
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.162
ELB improved by 0.0674918
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.107
ELB improved by 0.0553801
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.061
ELB improved by 0.0460582
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.022
ELB improved by 0.0387747
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.989
ELB improved by 0.0329973
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.961
ELB improved by 0.0283462
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.936
ELB improved by 0.0245479
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.915
ELB improved by 0.0214043
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.896
ELB improved by 0.0187705
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.879
ELB improved by 0.0165403
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.865
ELB improved by 0.014635
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.852
ELB improved by 0.0129957
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.84
ELB improved by 0.0115777
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.83
ELB improved by 0.0103463
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.82
ELB improved by 0.00927389
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-840.47
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-607.776
ELB improved by 232.694
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-549.741
ELB improved by 58.0351
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-496.335
ELB improved by 53.4055
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.284
ELB improved by 34.0512
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.094
ELB improved by 14.1898
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.919
ELB improved by 6.17471
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.858
ELB improved by 4.06174
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.392
ELB improved by 3.46554
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.993
ELB improved by 3.39894
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.398
ELB improved by 3.5953
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.465
ELB improved by 3.93263
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.21
ELB improved by 4.25488
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.92
ELB improved by 4.29055
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.108
ELB improved by 3.81168
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.179
ELB improved by 2.92891
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.158
ELB improved by 2.0215
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.809
ELB improved by 1.34872
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.878
ELB improved by 0.931078
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.188
ELB improved by 0.690354
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.635
ELB improved by 0.553056
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.161
ELB improved by 0.47314
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.736
ELB improved by 0.425409
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.339
ELB improved by 0.396555
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.96
ELB improved by 0.379584
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.589
ELB improved by 0.370936
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.22
ELB improved by 0.369128
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.846
ELB improved by 0.374087
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.459
ELB improved by 0.386498
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.053
ELB improved by 0.406666
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.619
ELB improved by 0.433568
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.152
ELB improved by 0.466486
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.643
ELB improved by 0.509719
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.07
ELB improved by 0.572963
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.415
ELB improved by 0.654981
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.699
ELB improved by 0.715993
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.989
ELB improved by 0.710207
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.328
ELB improved by 0.661086
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.715
ELB improved by 0.61267
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.137
ELB improved by 0.577926
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.58
ELB improved by 0.557145
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.026
ELB improved by 0.553988
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.444
ELB improved by 0.581509
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.782
ELB improved by 0.662011
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.003
ELB improved by 0.779524
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.21
ELB improved by 0.792686
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.556
ELB improved by 0.653948
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.062
ELB improved by 0.494469
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.693
ELB improved by 0.368691
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.417
ELB improved by 0.27567
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.209
ELB improved by 0.208607
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.047
ELB improved by 0.161235
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.92
ELB improved by 0.127928
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.815
ELB improved by 0.104041
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.729
ELB improved by 0.0861747
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.657
ELB improved by 0.072109
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.597
ELB improved by 0.0605413
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.546
ELB improved by 0.0507899
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.503
ELB improved by 0.0425326
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.468
ELB improved by 0.0356049
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.438
ELB improved by 0.0298758
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.413
ELB improved by 0.0252011
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.391
ELB improved by 0.0214226
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.373
ELB improved by 0.018384
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.357
ELB improved by 0.0159437
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.343
ELB improved by 0.0139813
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.331
ELB improved by 0.0123979
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.319
ELB improved by 0.0111147
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.309
ELB improved by 0.0100691
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.3
ELB improved by 0.0092122
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
0.989 0.077 1.065
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.012 | 0.004 | 0.016 | |
| getPIPs | 0.010 | 0.004 | 0.013 | |
| graper | 0.017 | 0.005 | 0.022 | |
| makeExampleData | 0.001 | 0.001 | 0.002 | |
| makeExampleDataWithUnequalGroups | 0.001 | 0.000 | 0.002 | |
| plotELBO | 0.101 | 0.006 | 0.108 | |
| plotGroupPenalties | 0.328 | 0.007 | 0.341 | |
| plotPosterior | 0.293 | 0.013 | 0.305 | |
| predict.graper | 0.213 | 0.053 | 0.266 | |
| print.graper | 0.010 | 0.003 | 0.013 | |