Britta Velten
| Snapshot Date: 2025-09-30 13:45 -0400 (Tue, 30 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 82b0592 |
| git_last_commit_date: 2025-06-24 03:15:40 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-01 12:07 -0400 (Wed, 01 Oct 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" | 4843 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4631 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4575 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
| 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 914/2337 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.25.2 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: graper |
| Version: 1.25.2 |
| 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_1.25.2.tar.gz |
| StartedAt: 2025-09-30 08:56:34 -0000 (Tue, 30 Sep 2025) |
| EndedAt: 2025-09-30 08:57:47 -0000 (Tue, 30 Sep 2025) |
| EllapsedTime: 73.1 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_1.25.2.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 ‘1.25.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘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 ‘1.25.2’ ** 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=-875.671
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.355
ELB improved by 291.316
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.137
ELB improved by 61.218
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.975
ELB improved by 41.1623
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.874
ELB improved by 18.1006
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.333
ELB improved by 7.54074
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.261
ELB improved by 5.0724
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.362
ELB improved by 4.8985
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.999
ELB improved by 5.36375
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.149
ELB improved by 5.8499
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.435
ELB improved by 5.71424
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.804
ELB improved by 4.63078
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.722
ELB improved by 3.08141
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.955
ELB improved by 1.76758
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.986
ELB improved by 0.968492
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.417
ELB improved by 0.568941
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.038
ELB improved by 0.379263
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.752
ELB improved by 0.286562
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.513
ELB improved by 0.238833
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.3
ELB improved by 0.212862
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.102
ELB improved by 0.197815
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.914
ELB improved by 0.188336
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.732
ELB improved by 0.18164
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.556
ELB improved by 0.176246
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.384
ELB improved by 0.17138
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.218
ELB improved by 0.166673
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.056
ELB improved by 0.161989
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.898
ELB improved by 0.157328
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.746
ELB improved by 0.152756
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.597
ELB improved by 0.148368
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.453
ELB improved by 0.144252
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.313
ELB improved by 0.140483
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.175
ELB improved by 0.13711
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.041
ELB improved by 0.134155
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.91
ELB improved by 0.131617
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.78
ELB improved by 0.129471
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.653
ELB improved by 0.127675
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.526
ELB improved by 0.126171
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.401
ELB improved by 0.124885
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.278
ELB improved by 0.123735
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.155
ELB improved by 0.122628
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.034
ELB improved by 0.121466
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.914
ELB improved by 0.120148
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.795
ELB improved by 0.118578
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.678
ELB improved by 0.116666
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.564
ELB improved by 0.114339
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.452
ELB improved by 0.111545
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.344
ELB improved by 0.108258
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.24
ELB improved by 0.104482
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.139
ELB improved by 0.100254
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.044
ELB improved by 0.0956373
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.953
ELB improved by 0.0907178
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.867
ELB improved by 0.0855969
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.787
ELB improved by 0.0803819
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.712
ELB improved by 0.0751765
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.642
ELB improved by 0.0700736
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.577
ELB improved by 0.0651496
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.516
ELB improved by 0.0604614
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.46
ELB improved by 0.0560455
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.408
ELB improved by 0.0519199
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.36
ELB improved by 0.0480867
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.316
ELB improved by 0.044536
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.274
ELB improved by 0.0412498
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.236
ELB improved by 0.0382059
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.201
ELB improved by 0.0353807
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.168
ELB improved by 0.0327522
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.138
ELB improved by 0.0303005
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.11
ELB improved by 0.0280096
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.084
ELB improved by 0.0258666
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.06
ELB improved by 0.0238616
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.038
ELB improved by 0.0219871
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.018
ELB improved by 0.020237
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.999
ELB improved by 0.0186064
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.982
ELB improved by 0.0170906
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.966
ELB improved by 0.0156852
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.952
ELB improved by 0.0143856
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.939
ELB improved by 0.0131869
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.927
ELB improved by 0.0120839
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.916
ELB improved by 0.0110714
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.906
ELB improved by 0.0101439
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.896
ELB improved by 0.00929598
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-865.011
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.027
ELB improved by 286.984
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.304
ELB improved by 62.723
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.582
ELB improved by 43.7215
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.731
ELB improved by 18.8517
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.464
ELB improved by 7.26646
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.583
ELB improved by 3.8813
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.917
ELB improved by 2.66589
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.688
ELB improved by 2.22897
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.651
ELB improved by 2.03719
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.711
ELB improved by 1.94033
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.825
ELB improved by 1.88514
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.978
ELB improved by 1.84704
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.166
ELB improved by 1.81253
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.393
ELB improved by 1.77236
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.674
ELB improved by 1.71941
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.027
ELB improved by 1.6471
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.481
ELB improved by 1.54633
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.075
ELB improved by 1.40592
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.848
ELB improved by 1.22643
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.815
ELB improved by 1.0332
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.954
ELB improved by 0.861188
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.226
ELB improved by 0.728178
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.596
ELB improved by 0.629719
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.039
ELB improved by 0.557278
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.529
ELB improved by 0.510156
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.043
ELB improved by 0.485573
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.575
ELB improved by 0.468368
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.133
ELB improved by 0.44164
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.722
ELB improved by 0.410552
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.331
ELB improved by 0.391818
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.943
ELB improved by 0.388024
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.549
ELB improved by 0.393656
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.144
ELB improved by 0.405154
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.722
ELB improved by 0.421552
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.279
ELB improved by 0.443182
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.808
ELB improved by 0.470881
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.303
ELB improved by 0.505463
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.755
ELB improved by 0.547198
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.16
ELB improved by 0.59525
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.513
ELB improved by 0.647123
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.815
ELB improved by 0.698328
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.072
ELB improved by 0.742712
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.298
ELB improved by 0.773849
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.511
ELB improved by 0.786907
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.733
ELB improved by 0.778639
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.988
ELB improved by 0.744844
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.305
ELB improved by 0.682468
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.707
ELB improved by 0.598052
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.201
ELB improved by 0.506361
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.781
ELB improved by 0.419866
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.437
ELB improved by 0.344066
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.158
ELB improved by 0.278954
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.935
ELB improved by 0.222654
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.761
ELB improved by 0.174508
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.625
ELB improved by 0.135611
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.518
ELB improved by 0.10688
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.431
ELB improved by 0.0874212
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.356
ELB improved by 0.0749382
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.289
ELB improved by 0.0668326
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.228
ELB improved by 0.0607205
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.174
ELB improved by 0.0546096
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.127
ELB improved by 0.0472608
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.088
ELB improved by 0.0386397
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.058
ELB improved by 0.0298138
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.036
ELB improved by 0.0220947
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.02
ELB improved by 0.0161961
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.008
ELB improved by 0.0120926
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.998
ELB improved by 0.00937326
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-878.819
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-596.363
ELB improved by 282.456
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-532.643
ELB improved by 63.7205
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.17
ELB improved by 51.4727
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.304
ELB improved by 26.8666
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.395
ELB improved by 9.90901
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.152
ELB improved by 5.24217
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.887
ELB improved by 4.26539
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.771
ELB improved by 4.1165
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.509
ELB improved by 4.2614
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.982
ELB improved by 4.52704
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.166
ELB improved by 4.8164
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.175
ELB improved by 4.99109
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.338
ELB improved by 4.8366
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.078
ELB improved by 4.25957
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.58
ELB improved by 3.49863
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.786
ELB improved by 2.79353
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.695
ELB improved by 2.09157
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.288
ELB improved by 1.40693
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.389
ELB improved by 0.898928
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.791
ELB improved by 0.597831
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.359
ELB improved by 0.432042
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.02
ELB improved by 0.338682
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.737
ELB improved by 0.283103
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.489
ELB improved by 0.248276
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.263
ELB improved by 0.22589
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.051
ELB improved by 0.211744
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.848
ELB improved by 0.203621
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.647
ELB improved by 0.200328
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.446
ELB improved by 0.201251
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.24
ELB improved by 0.206156
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.025
ELB improved by 0.215101
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.796
ELB improved by 0.228406
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.55
ELB improved by 0.246661
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.279
ELB improved by 0.270747
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.977
ELB improved by 0.301849
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.636
ELB improved by 0.341465
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.244
ELB improved by 0.391357
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.791
ELB improved by 0.453453
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.261
ELB improved by 0.529628
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.64
ELB improved by 0.621181
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.913
ELB improved by 0.727471
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.07
ELB improved by 0.842962
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.117
ELB improved by 0.95307
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.083
ELB improved by 1.0335
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.021
ELB improved by 1.06156
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.982
ELB improved by 1.03972
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.969
ELB improved by 1.01237
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.954
ELB improved by 1.01569
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.013
ELB improved by 0.941173
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.228
ELB improved by 0.784485
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.467
ELB improved by 0.760832
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.507
ELB improved by 0.96022
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.472
ELB improved by 1.03512
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.809
ELB improved by 0.662976
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.477
ELB improved by 0.331432
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.31
ELB improved by 0.167431
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.215
ELB improved by 0.0945937
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.154
ELB improved by 0.0611406
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.11
ELB improved by 0.0439408
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.077
ELB improved by 0.0338234
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.049
ELB improved by 0.0271851
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.027
ELB improved by 0.0224973
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.008
ELB improved by 0.0190243
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.991
ELB improved by 0.016365
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.977
ELB improved by 0.0142791
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.965
ELB improved by 0.0126125
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.953
ELB improved by 0.0112615
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.943
ELB improved by 0.0101537
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.934
ELB improved by 0.00923676
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-884.593
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.851
ELB improved by 303.742
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-520.862
ELB improved by 59.9894
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.112
ELB improved by 34.75
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.398
ELB improved by 14.7132
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.002
ELB improved by 6.39649
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.725
ELB improved by 4.27726
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.971
ELB improved by 3.75355
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.29
ELB improved by 3.68142
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.448
ELB improved by 3.8418
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.348
ELB improved by 4.1002
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.137
ELB improved by 4.21117
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.231
ELB improved by 3.90522
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.02
ELB improved by 3.21163
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.553
ELB improved by 2.46719
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.626
ELB improved by 1.92639
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.075
ELB improved by 1.55137
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.83
ELB improved by 1.24515
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.786
ELB improved by 1.04331
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.843
ELB improved by 0.943781
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.944
ELB improved by 0.898171
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.073
ELB improved by 0.871239
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.226
ELB improved by 0.846968
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.405
ELB improved by 0.820721
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.612
ELB improved by 0.793162
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.846
ELB improved by 0.766387
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.104
ELB improved by 0.741727
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.385
ELB improved by 0.718918
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.689
ELB improved by 0.69621
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.018
ELB improved by 0.670994
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.377
ELB improved by 0.640632
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.774
ELB improved by 0.603265
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.216
ELB improved by 0.558396
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.709
ELB improved by 0.507093
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.257
ELB improved by 0.451856
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.861
ELB improved by 0.396192
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.517
ELB improved by 0.344013
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.218
ELB improved by 0.299041
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.953
ELB improved by 0.26442
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.711
ELB improved by 0.242503
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.476
ELB improved by 0.234169
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.24
ELB improved by 0.236906
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.996
ELB improved by 0.243521
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.749
ELB improved by 0.246652
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.507
ELB improved by 0.242279
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.285
ELB improved by 0.221996
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.103
ELB improved by 0.181989
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.966
ELB improved by 0.137017
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.865
ELB improved by 0.101442
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.787
ELB improved by 0.0775999
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.725
ELB improved by 0.0623897
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.672
ELB improved by 0.0525712
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.626
ELB improved by 0.0459624
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.585
ELB improved by 0.0412448
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.547
ELB improved by 0.0376278
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.513
ELB improved by 0.034638
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.481
ELB improved by 0.0320187
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.451
ELB improved by 0.0296731
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.423
ELB improved by 0.027613
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.397
ELB improved by 0.025905
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.373
ELB improved by 0.0246289
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.349
ELB improved by 0.0238604
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.325
ELB improved by 0.0236757
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.301
ELB improved by 0.0241656
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.276
ELB improved by 0.0254445
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.248
ELB improved by 0.0276332
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.217
ELB improved by 0.0307847
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.183
ELB improved by 0.0347086
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.144
ELB improved by 0.0387059
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.102
ELB improved by 0.0414336
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.061
ELB improved by 0.0413558
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.023
ELB improved by 0.0378502
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.991
ELB improved by 0.0319067
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.966
ELB improved by 0.0254058
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.946
ELB improved by 0.0198152
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.93
ELB improved by 0.0156672
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.918
ELB improved by 0.0128456
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.907
ELB improved by 0.0110126
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.897
ELB improved by 0.00984927
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.903 0.164 3.058
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.046 | 0.008 | 0.055 | |
| getPIPs | 0.047 | 0.000 | 0.047 | |
| graper | 0.070 | 0.004 | 0.074 | |
| makeExampleData | 0.006 | 0.003 | 0.009 | |
| makeExampleDataWithUnequalGroups | 0.01 | 0.00 | 0.01 | |
| plotELBO | 0.420 | 0.016 | 0.437 | |
| plotGroupPenalties | 1.547 | 0.052 | 1.602 | |
| plotPosterior | 0.970 | 0.000 | 0.972 | |
| predict.graper | 1.010 | 0.032 | 1.043 | |
| print.graper | 0.039 | 0.008 | 0.047 | |