Britta Velten
| Snapshot Date: 2026-04-15 13:40 -0400 (Wed, 15 Apr 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 2026-04-16 11:35 -0400 (Thu, 16 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4928 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4659 |
| 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 936/2394 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| 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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz |
| StartedAt: 2026-04-16 00:34:01 -0400 (Thu, 16 Apr 2026) |
| EndedAt: 2026-04-16 00:35:33 -0400 (Thu, 16 Apr 2026) |
| EllapsedTime: 92.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-16 04:34:01 UTC
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-bioc/R/site-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 4.6.0 alpha (2026-04-05 r89794)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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=-883.441
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-582.468
ELB improved by 300.972
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.594
ELB improved by 56.8746
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.894
ELB improved by 34.6998
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.212
ELB improved by 14.6819
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.547
ELB improved by 6.66513
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.418
ELB improved by 4.12941
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.034
ELB improved by 3.38371
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.929
ELB improved by 3.10462
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.966
ELB improved by 2.9634
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.102
ELB improved by 2.86352
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.35
ELB improved by 2.75213
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.766
ELB improved by 2.58371
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.443
ELB improved by 2.32307
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.479
ELB improved by 1.96462
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.925
ELB improved by 1.55376
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.759
ELB improved by 1.16604
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.905
ELB improved by 0.85398
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.277
ELB improved by 0.628011
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.804
ELB improved by 0.47328
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.435
ELB improved by 0.368896
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.137
ELB improved by 0.297346
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.891
ELB improved by 0.246573
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.682
ELB improved by 0.20903
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.502
ELB improved by 0.180179
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.344
ELB improved by 0.157297
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.206
ELB improved by 0.138716
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.082
ELB improved by 0.123367
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.972
ELB improved by 0.110538
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.872
ELB improved by 0.0997242
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.781
ELB improved by 0.0905543
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.699
ELB improved by 0.0827457
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.623
ELB improved by 0.0760771
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.552
ELB improved by 0.070373
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.487
ELB improved by 0.0654923
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.425
ELB improved by 0.0613212
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.368
ELB improved by 0.0577675
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.313
ELB improved by 0.054757
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.261
ELB improved by 0.0522298
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.211
ELB improved by 0.0501384
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.162
ELB improved by 0.0484461
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.115
ELB improved by 0.0471253
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.069
ELB improved by 0.0461571
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.023
ELB improved by 0.0455306
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.978
ELB improved by 0.0452435
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.933
ELB improved by 0.0453017
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.887
ELB improved by 0.0457211
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.841
ELB improved by 0.0465284
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.793
ELB improved by 0.047764
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.743
ELB improved by 0.0494854
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.691
ELB improved by 0.0517722
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.637
ELB improved by 0.0547336
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.578
ELB improved by 0.0585196
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.515
ELB improved by 0.0633367
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.445
ELB improved by 0.0694732
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.368
ELB improved by 0.0773363
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.281
ELB improved by 0.087511
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.18
ELB improved by 0.100853
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.061
ELB improved by 0.118633
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.918
ELB improved by 0.142777
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.742
ELB improved by 0.17622
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.519
ELB improved by 0.223462
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.227
ELB improved by 0.291293
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.838
ELB improved by 0.389558
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.306
ELB improved by 0.531356
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.575
ELB improved by 0.731777
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.57
ELB improved by 1.0048
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.219
ELB improved by 1.35099
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.505
ELB improved by 1.71352
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.556
ELB improved by 1.94945
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.628
ELB improved by 1.92831
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.98
ELB improved by 1.64774
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.75
ELB improved by 1.23022
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.919
ELB improved by 0.83066
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.385
ELB improved by 0.534438
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.04
ELB improved by 0.344172
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.812
ELB improved by 0.228522
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.654
ELB improved by 0.158034
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.54
ELB improved by 0.113801
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.455
ELB improved by 0.0850516
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.389
ELB improved by 0.0657317
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.337
ELB improved by 0.0523339
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.294
ELB improved by 0.04274
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.259
ELB improved by 0.0356262
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.228
ELB improved by 0.0301514
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.203
ELB improved by 0.0257848
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.18
ELB improved by 0.0222012
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.161
ELB improved by 0.019209
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.144
ELB improved by 0.0166962
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.13
ELB improved by 0.014591
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.117
ELB improved by 0.0128382
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.106
ELB improved by 0.0113874
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.095
ELB improved by 0.0101906
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.086
ELB improved by 0.00920333
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.842
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-565.866
ELB improved by 290.976
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.566
ELB improved by 54.3004
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.818
ELB improved by 30.7475
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.796
ELB improved by 14.0218
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.285
ELB improved by 7.51106
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.274
ELB improved by 5.01181
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.974
ELB improved by 4.29909
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.923
ELB improved by 4.05165
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.239
ELB improved by 3.68419
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.161
ELB improved by 3.07708
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.772
ELB improved by 2.38963
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.956
ELB improved by 1.81574
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.528
ELB improved by 1.42791
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.325
ELB improved by 1.20296
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.244
ELB improved by 1.0817
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.243
ELB improved by 1.00051
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.314
ELB improved by 0.928816
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.449
ELB improved by 0.864843
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.642
ELB improved by 0.807466
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.887
ELB improved by 0.754724
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.177
ELB improved by 0.709758
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.499
ELB improved by 0.678662
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.831
ELB improved by 0.667778
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.144
ELB improved by 0.686815
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.388
ELB improved by 0.755809
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.482
ELB improved by 0.906743
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.335
ELB improved by 1.14686
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.905
ELB improved by 1.42963
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.2
ELB improved by 1.70514
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.42
ELB improved by 1.77999
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.839
ELB improved by 1.58113
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.521
ELB improved by 1.31819
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.412
ELB improved by 1.10907
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.488
ELB improved by 0.923597
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.751
ELB improved by 0.736851
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.181
ELB improved by 0.570533
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.731
ELB improved by 0.44941
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.344
ELB improved by 0.387467
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.951
ELB improved by 0.393059
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.506
ELB improved by 0.445055
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.041
ELB improved by 0.464311
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.639
ELB improved by 0.402538
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.341
ELB improved by 0.298291
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.138
ELB improved by 0.202516
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.002
ELB improved by 0.135696
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.909
ELB improved by 0.0934261
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.842
ELB improved by 0.0667031
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.793
ELB improved by 0.0493443
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.755
ELB improved by 0.0377535
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.725
ELB improved by 0.0298191
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.701
ELB improved by 0.0242512
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.681
ELB improved by 0.0202393
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.664
ELB improved by 0.017266
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.649
ELB improved by 0.0149977
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.635
ELB improved by 0.0132179
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.624
ELB improved by 0.0117846
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.613
ELB improved by 0.0106036
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.603
ELB improved by 0.00961179
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-884.309
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.098
ELB improved by 306.211
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.214
ELB improved by 61.8835
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.763
ELB improved by 39.4516
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.654
ELB improved by 18.1086
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.472
ELB improved by 7.1819
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.456
ELB improved by 4.01642
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.422
ELB improved by 3.03393
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.75
ELB improved by 2.67195
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.192
ELB improved by 2.5582
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.636
ELB improved by 2.55577
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.033
ELB improved by 2.60307
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.385
ELB improved by 2.64772
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.766
ELB improved by 2.61928
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.32
ELB improved by 2.44611
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.21
ELB improved by 2.10964
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.523
ELB improved by 1.68726
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.211
ELB improved by 1.31212
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.134
ELB improved by 1.07733
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.146
ELB improved by 0.987892
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.179
ELB improved by 0.966403
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.233
ELB improved by 0.946246
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.281
ELB improved by 0.951503
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.271
ELB improved by 1.01075
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.148
ELB improved by 1.12291
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.893
ELB improved by 1.2547
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.543
ELB improved by 1.35004
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.12
ELB improved by 1.42329
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.545
ELB improved by 1.57452
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.701
ELB improved by 1.84437
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.658
ELB improved by 2.0432
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.582
ELB improved by 2.07571
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.51
ELB improved by 2.07157
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.457
ELB improved by 2.05385
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.607
ELB improved by 1.84998
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.259
ELB improved by 1.3474
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.41
ELB improved by 0.849482
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.882
ELB improved by 0.528169
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.536
ELB improved by 0.345809
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.295
ELB improved by 0.241193
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.117
ELB improved by 0.177275
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.982
ELB improved by 0.13554
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.875
ELB improved by 0.106803
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.789
ELB improved by 0.0862084
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.718
ELB improved by 0.0709818
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.658
ELB improved by 0.0594317
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.608
ELB improved by 0.0504756
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.564
ELB improved by 0.0433956
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.527
ELB improved by 0.0377017
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.494
ELB improved by 0.0330521
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.464
ELB improved by 0.0292035
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.438
ELB improved by 0.0259795
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.415
ELB improved by 0.02325
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.394
ELB improved by 0.0209177
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.375
ELB improved by 0.0189088
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.358
ELB improved by 0.0171661
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.343
ELB improved by 0.0156451
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.328
ELB improved by 0.0143106
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.315
ELB improved by 0.0131341
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.303
ELB improved by 0.0120927
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.292
ELB improved by 0.0111676
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.282
ELB improved by 0.0103431
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.272
ELB improved by 0.00960608
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-888.701
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.987
ELB improved by 309.715
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.41
ELB improved by 64.5762
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.954
ELB improved by 46.4561
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.459
ELB improved by 22.495
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.523
ELB improved by 9.93603
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.703
ELB improved by 5.82068
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.62
ELB improved by 4.08271
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.272
ELB improved by 3.34755
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.09
ELB improved by 3.18234
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.725
ELB improved by 3.3655
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.943
ELB improved by 3.7812
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.63
ELB improved by 4.3135
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.918
ELB improved by 4.7122
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.342
ELB improved by 4.57544
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.632
ELB improved by 3.71043
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.135
ELB improved by 2.49627
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.646
ELB improved by 1.48939
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.772
ELB improved by 0.873913
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.229
ELB improved by 0.543457
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.861
ELB improved by 0.367216
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.592
ELB improved by 0.269018
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.381
ELB improved by 0.211874
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.202
ELB improved by 0.178114
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.043
ELB improved by 0.159187
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.892
ELB improved by 0.151332
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.738
ELB improved by 0.153952
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.569
ELB improved by 0.16915
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.368
ELB improved by 0.200745
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.119
ELB improved by 0.249606
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.812
ELB improved by 0.306605
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.452
ELB improved by 0.360072
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.04
ELB improved by 0.412005
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.575
ELB improved by 0.465293
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.071
ELB improved by 0.504028
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.564
ELB improved by 0.506342
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.088
ELB improved by 0.475782
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.654
ELB improved by 0.434537
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.258
ELB improved by 0.396119
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.894
ELB improved by 0.363939
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.555
ELB improved by 0.338599
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.235
ELB improved by 0.320176
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.927
ELB improved by 0.308376
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.624
ELB improved by 0.302559
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.322
ELB improved by 0.301792
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.017
ELB improved by 0.304866
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.707
ELB improved by 0.310275
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.391
ELB improved by 0.316232
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.07
ELB improved by 0.320781
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.748
ELB improved by 0.322019
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.43
ELB improved by 0.318347
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.121
ELB improved by 0.308663
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.829
ELB improved by 0.292476
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.559
ELB improved by 0.270126
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.315
ELB improved by 0.243153
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.101
ELB improved by 0.214434
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.913
ELB improved by 0.187607
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.747
ELB improved by 0.165947
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.596
ELB improved by 0.151035
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.455
ELB improved by 0.141214
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.324
ELB improved by 0.130686
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.212
ELB improved by 0.112874
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.124
ELB improved by 0.0878809
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.061
ELB improved by 0.0628236
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.017
ELB improved by 0.0434696
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.987
ELB improved by 0.0306151
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.964
ELB improved by 0.0226082
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.946
ELB improved by 0.0176843
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.932
ELB improved by 0.0146195
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.919
ELB improved by 0.0126699
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.908
ELB improved by 0.0114002
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.897
ELB improved by 0.0105558
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.887
ELB improved by 0.00998528
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.476 0.206 2.669
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.057 | 0.015 | 0.073 | |
| getPIPs | 0.072 | 0.028 | 0.101 | |
| graper | 0.081 | 0.022 | 0.103 | |
| makeExampleData | 0.01 | 0.00 | 0.01 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.001 | 0.012 | |
| plotELBO | 0.307 | 0.025 | 0.332 | |
| plotGroupPenalties | 0.996 | 0.013 | 1.008 | |
| plotPosterior | 0.696 | 0.010 | 0.705 | |
| predict.graper | 2.061 | 0.089 | 2.153 | |
| print.graper | 0.056 | 0.011 | 0.066 | |