Britta Velten
| Snapshot Date: 2025-11-11 13:45 -0500 (Tue, 11 Nov 2025) |
| 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 2025-11-12 11:58 -0500 (Wed, 12 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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: 2025-11-11 10:25:01 -0000 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 10:26:17 -0000 (Tue, 11 Nov 2025) |
| EllapsedTime: 76.1 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=-870.881
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-568.096
ELB improved by 302.785
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-509.314
ELB improved by 58.782
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.734
ELB improved by 33.5798
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.699
ELB improved by 14.0349
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.264
ELB improved by 6.43492
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.575
ELB improved by 4.68938
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.09
ELB improved by 4.48518
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.408
ELB improved by 4.68118
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.342
ELB improved by 5.06652
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.867
ELB improved by 5.475
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.268
ELB improved by 5.59881
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.17
ELB improved by 5.09779
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.145
ELB improved by 4.02544
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.295
ELB improved by 2.84989
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.373
ELB improved by 1.92183
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.07
ELB improved by 1.30294
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.155
ELB improved by 0.91511
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.485
ELB improved by 0.670393
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.97
ELB improved by 0.514812
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.553
ELB improved by 0.417278
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.196
ELB improved by 0.357077
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.875
ELB improved by 0.320614
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.575
ELB improved by 0.299864
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.285
ELB improved by 0.290478
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.994
ELB improved by 0.29024
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.696
ELB improved by 0.298181
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.382
ELB improved by 0.314158
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.043
ELB improved by 0.338749
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.67
ELB improved by 0.373396
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.249
ELB improved by 0.420839
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.763
ELB improved by 0.486065
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.185
ELB improved by 0.578067
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.473
ELB improved by 0.711872
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.57
ELB improved by 0.903108
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.441
ELB improved by 1.12921
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.148
ELB improved by 1.29252
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.801
ELB improved by 1.34757
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.469
ELB improved by 1.33165
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.227
ELB improved by 1.24165
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.15
ELB improved by 1.07741
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.275
ELB improved by 0.874629
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.597
ELB improved by 0.678032
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.083
ELB improved by 0.514508
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.693
ELB improved by 0.390144
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.393
ELB improved by 0.299613
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.159
ELB improved by 0.23436
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.972
ELB improved by 0.186415
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.823
ELB improved by 0.1497
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.702
ELB improved by 0.120335
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.606
ELB improved by 0.0963298
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.529
ELB improved by 0.0768014
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.468
ELB improved by 0.061196
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.419
ELB improved by 0.0489251
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.38
ELB improved by 0.0393596
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.348
ELB improved by 0.03192
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.322
ELB improved by 0.0261248
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.3
ELB improved by 0.0215939
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.282
ELB improved by 0.0180336
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.267
ELB improved by 0.0152192
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.254
ELB improved by 0.0129792
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.243
ELB improved by 0.0111837
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.233
ELB improved by 0.00973384
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-875.812
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.466
ELB improved by 297.346
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.202
ELB improved by 61.2638
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.682
ELB improved by 35.5196
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.399
ELB improved by 14.2833
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.249
ELB improved by 6.1498
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.757
ELB improved by 3.49197
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.209
ELB improved by 2.54784
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.026
ELB improved by 2.18297
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.004
ELB improved by 2.02254
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.086
ELB improved by 1.91818
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.273
ELB improved by 1.813
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.592
ELB improved by 1.68047
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.081
ELB improved by 1.51158
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.766
ELB improved by 1.31416
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.657
ELB improved by 1.10944
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.734
ELB improved by 0.923012
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.961
ELB improved by 0.773299
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.295
ELB improved by 0.665788
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.699
ELB improved by 0.595899
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.144
ELB improved by 0.554815
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.61
ELB improved by 0.533627
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.085
ELB improved by 0.525117
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.561
ELB improved by 0.524143
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.034
ELB improved by 0.527442
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.501
ELB improved by 0.533227
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.96
ELB improved by 0.540729
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.41
ELB improved by 0.549724
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.85
ELB improved by 0.560087
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.279
ELB improved by 0.571418
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.696
ELB improved by 0.58276
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.103
ELB improved by 0.59246
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.505
ELB improved by 0.598224
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.908
ELB improved by 0.597433
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.32
ELB improved by 0.587718
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.752
ELB improved by 0.567642
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.215
ELB improved by 0.53717
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.718
ELB improved by 0.497671
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.266
ELB improved by 0.451618
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.864
ELB improved by 0.402371
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.51
ELB improved by 0.353942
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.199
ELB improved by 0.310302
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.925
ELB improved by 0.274484
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.677
ELB improved by 0.24808
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.446
ELB improved by 0.231197
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.223
ELB improved by 0.222572
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.004
ELB improved by 0.219397
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.787
ELB improved by 0.216433
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.581
ELB improved by 0.205969
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.398
ELB improved by 0.18292
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.247
ELB improved by 0.151338
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.126
ELB improved by 0.120817
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.029
ELB improved by 0.0972443
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.948
ELB improved by 0.0806692
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.879
ELB improved by 0.068805
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.82
ELB improved by 0.0596644
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.768
ELB improved by 0.0521328
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.722
ELB improved by 0.0457132
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.682
ELB improved by 0.0402084
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.646
ELB improved by 0.0355235
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.615
ELB improved by 0.0315762
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.586
ELB improved by 0.0282713
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.561
ELB improved by 0.0255053
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.538
ELB improved by 0.0231772
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.516
ELB improved by 0.0211972
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.497
ELB improved by 0.0194905
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.479
ELB improved by 0.0179978
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.462
ELB improved by 0.016673
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.447
ELB improved by 0.0154813
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.432
ELB improved by 0.0143968
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.419
ELB improved by 0.0134003
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.406
ELB improved by 0.0124783
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.395
ELB improved by 0.0116213
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.384
ELB improved by 0.0108231
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.374
ELB improved by 0.0100798
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.365
ELB improved by 0.00938891
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-847.194
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-550.61
ELB improved by 296.584
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.596
ELB improved by 60.0136
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.683
ELB improved by 36.9127
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.696
ELB improved by 15.9877
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.185
ELB improved by 7.51042
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.199
ELB improved by 4.98647
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.008
ELB improved by 4.19031
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.91
ELB improved by 4.09847
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.561
ELB improved by 4.34866
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.866
ELB improved by 4.69486
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.032
ELB improved by 4.83438
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.59
ELB improved by 4.44211
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.086
ELB improved by 3.50392
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.665
ELB improved by 2.4214
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.083
ELB improved by 1.58151
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.018
ELB improved by 1.06551
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.243
ELB improved by 0.774657
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.636
ELB improved by 0.607438
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.13
ELB improved by 0.505242
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.692
ELB improved by 0.438593
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.299
ELB improved by 0.392331
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.941
ELB improved by 0.358116
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.61
ELB improved by 0.331093
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.302
ELB improved by 0.308368
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.014
ELB improved by 0.288261
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.744
ELB improved by 0.269891
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.491
ELB improved by 0.25291
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.253
ELB improved by 0.237305
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.03
ELB improved by 0.223232
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.819
ELB improved by 0.210889
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.619
ELB improved by 0.200421
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.427
ELB improved by 0.191869
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.242
ELB improved by 0.185169
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.062
ELB improved by 0.180213
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.885
ELB improved by 0.176915
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.709
ELB improved by 0.175229
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.534
ELB improved by 0.175082
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.358
ELB improved by 0.176418
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.178
ELB improved by 0.17961
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.992
ELB improved by 0.186335
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.791
ELB improved by 0.200913
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.558
ELB improved by 0.232808
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.256
ELB improved by 0.30205
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.81
ELB improved by 0.445761
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.101
ELB improved by 0.70965
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.961
ELB improved by 1.14027
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.09
ELB improved by 1.87072
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.429
ELB improved by 2.66128
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.8
ELB improved by 2.62896
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.611
ELB improved by 2.18868
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.859
ELB improved by 1.7522
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.513
ELB improved by 1.34611
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.543
ELB improved by 0.969152
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.903
ELB improved by 0.640054
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.514
ELB improved by 0.389241
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.289
ELB improved by 0.224949
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.16
ELB improved by 0.129366
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.083
ELB improved by 0.077291
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.033
ELB improved by 0.0493639
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-364.999
ELB improved by 0.0340681
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-364.974
ELB improved by 0.0253036
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-364.954
ELB improved by 0.0199712
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-364.937
ELB improved by 0.0165014
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-364.923
ELB improved by 0.0140869
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-364.911
ELB improved by 0.0123016
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-364.9
ELB improved by 0.0109142
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-364.89
ELB improved by 0.00979388
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-877.316
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-583.95
ELB improved by 293.365
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.228
ELB improved by 60.7224
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.912
ELB improved by 38.3158
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.492
ELB improved by 16.4198
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.262
ELB improved by 6.23064
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.738
ELB improved by 3.52413
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.936
ELB improved by 2.80122
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.424
ELB improved by 2.51231
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.089
ELB improved by 2.33501
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.897
ELB improved by 2.19231
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.844
ELB improved by 2.05237
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.948
ELB improved by 1.89595
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.238
ELB improved by 1.70992
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.747
ELB improved by 1.49128
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.495
ELB improved by 1.25184
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.481
ELB improved by 1.01404
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.681
ELB improved by 0.800552
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.055
ELB improved by 0.625359
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.564
ELB improved by 0.491399
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.17
ELB improved by 0.393818
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.845
ELB improved by 0.32473
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.569
ELB improved by 0.2765
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.326
ELB improved by 0.243061
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.106
ELB improved by 0.220051
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.901
ELB improved by 0.20449
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.707
ELB improved by 0.194397
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.518
ELB improved by 0.188473
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.333
ELB improved by 0.185859
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.147
ELB improved by 0.185977
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.958
ELB improved by 0.188426
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.765
ELB improved by 0.192914
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.566
ELB improved by 0.199228
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.359
ELB improved by 0.207211
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.142
ELB improved by 0.216771
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.914
ELB improved by 0.227891
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.674
ELB improved by 0.240659
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.418
ELB improved by 0.255304
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.146
ELB improved by 0.272238
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.854
ELB improved by 0.292101
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.538
ELB improved by 0.315802
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.194
ELB improved by 0.344531
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.814
ELB improved by 0.379727
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.391
ELB improved by 0.422963
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.915
ELB improved by 0.475702
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.376
ELB improved by 0.53909
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.762
ELB improved by 0.614377
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.056
ELB improved by 0.705402
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.232
ELB improved by 0.824602
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.233
ELB improved by 0.998176
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.992
ELB improved by 1.24176
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.525
ELB improved by 1.46634
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.051
ELB improved by 1.47424
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.813
ELB improved by 1.23863
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.894
ELB improved by 0.91806
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.262
ELB improved by 0.632093
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.841
ELB improved by 0.420989
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.561
ELB improved by 0.280049
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.371
ELB improved by 0.190009
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.238
ELB improved by 0.132948
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.142
ELB improved by 0.0964151
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.069
ELB improved by 0.0726543
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.012
ELB improved by 0.0569713
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.966
ELB improved by 0.0464776
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.927
ELB improved by 0.0393112
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.892
ELB improved by 0.0342088
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.862
ELB improved by 0.0303053
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.835
ELB improved by 0.0270575
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.811
ELB improved by 0.0241937
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.789
ELB improved by 0.0216367
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.77
ELB improved by 0.019403
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.752
ELB improved by 0.017521
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.736
ELB improved by 0.0159926
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.721
ELB improved by 0.0147897
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.708
ELB improved by 0.0138666
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.694
ELB improved by 0.0131724
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.682
ELB improved by 0.0126576
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.669
ELB improved by 0.012276
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.657
ELB improved by 0.0119846
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.646
ELB improved by 0.0117413
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.634
ELB improved by 0.0115048
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.623
ELB improved by 0.0112359
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.612
ELB improved by 0.0109006
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.602
ELB improved by 0.0104754
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.592
ELB improved by 0.00995152
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.780 0.154 2.927
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.048 | 0.004 | 0.053 | |
| getPIPs | 0.043 | 0.004 | 0.047 | |
| graper | 0.073 | 0.000 | 0.073 | |
| makeExampleData | 0.008 | 0.000 | 0.008 | |
| makeExampleDataWithUnequalGroups | 0.01 | 0.00 | 0.01 | |
| plotELBO | 0.410 | 0.016 | 0.427 | |
| plotGroupPenalties | 1.562 | 0.028 | 1.593 | |
| plotPosterior | 1.006 | 0.180 | 1.189 | |
| predict.graper | 0.977 | 0.036 | 1.015 | |
| print.graper | 0.044 | 0.008 | 0.052 | |