Britta Velten
| Snapshot Date: 2026-01-05 13:45 -0500 (Mon, 05 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_22 |
| git_last_commit: 76fc31b |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-08 11:59 -0500 (Thu, 08 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 922/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.26.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: graper |
| Version: 1.26.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings graper_1.26.0.tar.gz |
| StartedAt: 2026-01-06 10:57:28 -0000 (Tue, 06 Jan 2026) |
| EndedAt: 2026-01-06 10:59:30 -0000 (Tue, 06 Jan 2026) |
| EllapsedTime: 122.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings graper_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.26.0’
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.8Mb
* 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 ... 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
‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.26.0’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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=-865.923
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.862
ELB improved by 287.061
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-521.138
ELB improved by 57.7241
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.72
ELB improved by 37.4177
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.928
ELB improved by 15.7922
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.472
ELB improved by 6.45577
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.131
ELB improved by 4.34094
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.149
ELB improved by 3.98246
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.089
ELB improved by 4.05939
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.738
ELB improved by 4.3517
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.961
ELB improved by 4.77615
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.846
ELB improved by 5.11538
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.866
ELB improved by 4.9805
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.675
ELB improved by 4.19103
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.623
ELB improved by 3.05165
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.602
ELB improved by 2.021
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.24
ELB improved by 1.36137
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.196
ELB improved by 1.04436
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.229
ELB improved by 0.966848
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.242
ELB improved by 0.987177
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.368
ELB improved by 0.873929
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.69
ELB improved by 0.678065
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.118
ELB improved by 0.571966
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.583
ELB improved by 0.534711
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.056
ELB improved by 0.527593
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.522
ELB improved by 0.533485
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.981
ELB improved by 0.540877
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.438
ELB improved by 0.543207
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.895
ELB improved by 0.543122
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.348
ELB improved by 0.547322
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.788
ELB improved by 0.559603
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.208
ELB improved by 0.580404
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.599
ELB improved by 0.608856
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.955
ELB improved by 0.644281
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.267
ELB improved by 0.687423
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.525
ELB improved by 0.741981
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.709
ELB improved by 0.816221
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.786
ELB improved by 0.923016
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.719
ELB improved by 1.06709
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.545
ELB improved by 1.17362
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.44
ELB improved by 1.10557
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.494
ELB improved by 0.945691
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.65
ELB improved by 0.844532
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.84
ELB improved by 0.809475
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.146
ELB improved by 0.694335
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.654
ELB improved by 0.491772
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.291
ELB improved by 0.362757
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.942
ELB improved by 0.348965
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.533
ELB improved by 0.408756
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.128
ELB improved by 0.405583
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.843
ELB improved by 0.285292
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.679
ELB improved by 0.163486
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.587
ELB improved by 0.0916882
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.532
ELB improved by 0.0556895
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.494
ELB improved by 0.0381688
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.464
ELB improved by 0.0293881
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.44
ELB improved by 0.024662
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.418
ELB improved by 0.0218423
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.398
ELB improved by 0.0199542
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.379
ELB improved by 0.0185499
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.362
ELB improved by 0.0174161
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.345
ELB improved by 0.0164462
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.33
ELB improved by 0.015583
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.315
ELB improved by 0.0147939
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.301
ELB improved by 0.0140592
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.288
ELB improved by 0.0133666
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.275
ELB improved by 0.0127083
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.263
ELB improved by 0.0120792
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.251
ELB improved by 0.0114761
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.24
ELB improved by 0.0108969
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.23
ELB improved by 0.0103405
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.22
ELB improved by 0.00980618
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-851.097
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.53
ELB improved by 286.566
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-500.827
ELB improved by 63.7033
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.242
ELB improved by 41.5849
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.534
ELB improved by 17.7081
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.993
ELB improved by 7.54105
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.849
ELB improved by 5.14419
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.192
ELB improved by 4.65686
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.234
ELB improved by 4.95735
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.617
ELB improved by 5.61793
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.469
ELB improved by 6.14743
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.519
ELB improved by 5.95051
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.637
ELB improved by 4.88181
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.073
ELB improved by 3.56334
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.421
ELB improved by 2.65279
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.222
ELB improved by 2.19823
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.382
ELB improved by 1.84075
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.834
ELB improved by 1.54809
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.493
ELB improved by 1.34063
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.404
ELB improved by 1.08901
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.516
ELB improved by 0.887587
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.748
ELB improved by 0.768675
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.056
ELB improved by 0.691333
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.422
ELB improved by 0.634209
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.829
ELB improved by 0.593383
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.254
ELB improved by 0.574294
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.664
ELB improved by 0.590253
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.009
ELB improved by 0.655084
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.265
ELB improved by 0.743787
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.477
ELB improved by 0.78815
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.68
ELB improved by 0.796952
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.858
ELB improved by 0.822644
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.978
ELB improved by 0.879799
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.013
ELB improved by 0.964449
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.952
ELB improved by 1.06121
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.832
ELB improved by 1.11965
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.778
ELB improved by 1.05489
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.914
ELB improved by 0.863888
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.271
ELB improved by 0.642328
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.816
ELB improved by 0.454982
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.5
ELB improved by 0.316513
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.279
ELB improved by 0.221018
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.122
ELB improved by 0.157137
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.007
ELB improved by 0.114481
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.922
ELB improved by 0.0855372
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.856
ELB improved by 0.06541
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.805
ELB improved by 0.0510373
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.765
ELB improved by 0.0405185
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.732
ELB improved by 0.0326604
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.705
ELB improved by 0.0266945
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.683
ELB improved by 0.0221083
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.665
ELB improved by 0.0185462
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.649
ELB improved by 0.0157537
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.635
ELB improved by 0.013544
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.624
ELB improved by 0.0117787
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.613
ELB improved by 0.0103543
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.604
ELB improved by 0.00919315
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-878.689
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.18
ELB improved by 292.508
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-530.822
ELB improved by 55.3583
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-494.428
ELB improved by 36.3945
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.182
ELB improved by 17.2458
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.961
ELB improved by 7.22119
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.519
ELB improved by 3.44193
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.214
ELB improved by 2.30458
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.293
ELB improved by 1.92125
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.536
ELB improved by 1.75686
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.88
ELB improved by 1.65572
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.334
ELB improved by 1.54572
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.947
ELB improved by 1.38794
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.771
ELB improved by 1.17508
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.839
ELB improved by 0.932773
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.137
ELB improved by 0.702184
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.622
ELB improved by 0.514081
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.245
ELB improved by 0.377115
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.961
ELB improved by 0.283962
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.739
ELB improved by 0.222256
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.558
ELB improved by 0.181129
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.405
ELB improved by 0.152976
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.272
ELB improved by 0.133005
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.154
ELB improved by 0.118323
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.046
ELB improved by 0.107194
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.948
ELB improved by 0.0985616
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.856
ELB improved by 0.0917584
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.77
ELB improved by 0.086352
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.688
ELB improved by 0.0820528
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.609
ELB improved by 0.0786638
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.533
ELB improved by 0.0760513
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.459
ELB improved by 0.0741271
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.386
ELB improved by 0.0728381
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.314
ELB improved by 0.0721591
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.242
ELB improved by 0.0720893
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.169
ELB improved by 0.0726502
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.095
ELB improved by 0.0738852
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.019
ELB improved by 0.0758628
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.941
ELB improved by 0.0786811
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.858
ELB improved by 0.0824772
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.771
ELB improved by 0.0874424
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.677
ELB improved by 0.0938411
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.575
ELB improved by 0.102032
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.462
ELB improved by 0.112486
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.337
ELB improved by 0.125771
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.194
ELB improved by 0.142504
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.031
ELB improved by 0.163201
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.843
ELB improved by 0.188054
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.626
ELB improved by 0.216689
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.378
ELB improved by 0.248136
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.097
ELB improved by 0.281236
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.781
ELB improved by 0.315417
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.43
ELB improved by 0.351366
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.039
ELB improved by 0.391126
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.601
ELB improved by 0.437636
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.107
ELB improved by 0.494058
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.544
ELB improved by 0.563039
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.898
ELB improved by 0.64581
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.157
ELB improved by 0.741032
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.314
ELB improved by 0.843744
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.368
ELB improved by 0.945873
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.326
ELB improved by 1.04182
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.183
ELB improved by 1.14316
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.895
ELB improved by 1.28731
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.427
ELB improved by 1.46815
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.823
ELB improved by 1.60446
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.114
ELB improved by 1.70889
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.439
ELB improved by 1.67526
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.958
ELB improved by 1.48022
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.717
ELB improved by 1.24126
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.805
ELB improved by 0.912197
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.243
ELB improved by 0.561634
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.914
ELB improved by 0.329778
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.697
ELB improved by 0.21692
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.529
ELB improved by 0.167274
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.386
ELB improved by 0.143048
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.262
ELB improved by 0.124289
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.159
ELB improved by 0.103143
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.078
ELB improved by 0.0807927
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.017
ELB improved by 0.0613398
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.97
ELB improved by 0.0467837
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.933
ELB improved by 0.0367312
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.903
ELB improved by 0.0299392
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.878
ELB improved by 0.0252673
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.856
ELB improved by 0.0219199
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.837
ELB improved by 0.0194011
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.819
ELB improved by 0.0174159
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.804
ELB improved by 0.0157912
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.789
ELB improved by 0.014424
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.776
ELB improved by 0.0132508
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.764
ELB improved by 0.0122308
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.752
ELB improved by 0.0113361
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.742
ELB improved by 0.0105461
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.732
ELB improved by 0.00984539
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-864.601
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-577.874
ELB improved by 286.727
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.824
ELB improved by 60.0505
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.705
ELB improved by 37.1189
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.825
ELB improved by 16.8797
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.351
ELB improved by 7.47375
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.829
ELB improved by 4.52249
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.88
ELB improved by 3.94865
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.883
ELB improved by 3.99683
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.677
ELB improved by 4.20628
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.318
ELB improved by 4.35956
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.065
ELB improved by 4.25235
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.324
ELB improved by 3.74106
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.397
ELB improved by 2.92687
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.254
ELB improved by 2.1437
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.673
ELB improved by 1.58073
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.458
ELB improved by 1.21491
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.475
ELB improved by 0.982859
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.637
ELB improved by 0.838213
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.902
ELB improved by 0.73461
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.266
ELB improved by 0.63637
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.722
ELB improved by 0.543373
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.249
ELB improved by 0.473673
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.818
ELB improved by 0.431059
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.41
ELB improved by 0.407351
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.016
ELB improved by 0.394444
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.628
ELB improved by 0.387617
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.244
ELB improved by 0.38461
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.859
ELB improved by 0.384459
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.472
ELB improved by 0.386818
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.081
ELB improved by 0.391637
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.682
ELB improved by 0.399009
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.273
ELB improved by 0.409093
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.851
ELB improved by 0.422035
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.413
ELB improved by 0.437827
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.957
ELB improved by 0.456083
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.481
ELB improved by 0.475766
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.986
ELB improved by 0.495005
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.475
ELB improved by 0.511165
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.954
ELB improved by 0.521239
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.431
ELB improved by 0.52242
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.919
ELB improved by 0.512622
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.428
ELB improved by 0.490827
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.97
ELB improved by 0.457338
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.556
ELB improved by 0.414033
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.192
ELB improved by 0.364347
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.879
ELB improved by 0.312592
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.617
ELB improved by 0.262841
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.399
ELB improved by 0.218002
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.219
ELB improved by 0.179532
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.071
ELB improved by 0.147705
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.949
ELB improved by 0.122101
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.847
ELB improved by 0.102012
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.761
ELB improved by 0.0866814
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.685
ELB improved by 0.075432
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.617
ELB improved by 0.067734
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.554
ELB improved by 0.06325
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.492
ELB improved by 0.0618477
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.429
ELB improved by 0.063536
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.361
ELB improved by 0.068196
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.286
ELB improved by 0.0748927
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.205
ELB improved by 0.080823
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.124
ELB improved by 0.0812775
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.051
ELB improved by 0.0728989
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.993
ELB improved by 0.0578941
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.951
ELB improved by 0.0422151
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.921
ELB improved by 0.0298482
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.899
ELB improved by 0.0213014
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.884
ELB improved by 0.0155995
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.872
ELB improved by 0.0117527
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.863
ELB improved by 0.00909208
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.866 0.189 3.048
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.051 | 0.000 | 0.051 | |
| getPIPs | 0.047 | 0.000 | 0.047 | |
| graper | 0.066 | 0.008 | 0.074 | |
| makeExampleData | 0.008 | 0.000 | 0.008 | |
| makeExampleDataWithUnequalGroups | 0.009 | 0.000 | 0.010 | |
| plotELBO | 0.394 | 0.016 | 0.411 | |
| plotGroupPenalties | 1.489 | 0.020 | 1.512 | |
| plotPosterior | 0.921 | 0.008 | 0.931 | |
| predict.graper | 0.993 | 0.020 | 1.015 | |
| print.graper | 0.044 | 0.003 | 0.047 | |