Britta Velten
| Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 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 2025-09-26 12:07 -0400 (Fri, 26 Sep 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" | 4831 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4619 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4563 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 913/2334 | 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: 2025-09-26 08:19:14 -0000 (Fri, 26 Sep 2025) |
| EndedAt: 2025-09-26 08:20:27 -0000 (Fri, 26 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=-891.294
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-568.808
ELB improved by 322.486
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-509.594
ELB improved by 59.2145
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.518
ELB improved by 37.0752
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.248
ELB improved by 16.2702
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.509
ELB improved by 7.73901
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.065
ELB improved by 5.44375
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.001
ELB improved by 5.06403
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.552
ELB improved by 5.4491
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.492
ELB improved by 6.06075
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.231
ELB improved by 6.26074
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.764
ELB improved by 5.46687
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.906
ELB improved by 3.85748
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.591
ELB improved by 2.31523
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.216
ELB improved by 1.37546
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.312
ELB improved by 0.903981
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.651
ELB improved by 0.660667
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.13
ELB improved by 0.521512
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.695
ELB improved by 0.434775
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.318
ELB improved by 0.377317
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.98
ELB improved by 0.337417
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.672
ELB improved by 0.308516
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.385
ELB improved by 0.286694
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.115
ELB improved by 0.26951
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.86
ELB improved by 0.255415
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.617
ELB improved by 0.243428
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.384
ELB improved by 0.232947
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.16
ELB improved by 0.223635
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.945
ELB improved by 0.215342
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.737
ELB improved by 0.208068
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.535
ELB improved by 0.201946
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.337
ELB improved by 0.197255
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.143
ELB improved by 0.194475
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.948
ELB improved by 0.194399
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.75
ELB improved by 0.198345
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.542
ELB improved by 0.208441
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.314
ELB improved by 0.227765
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.055
ELB improved by 0.259121
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.755
ELB improved by 0.299948
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.419
ELB improved by 0.335531
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.071
ELB improved by 0.347867
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.734
ELB improved by 0.3372
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.418
ELB improved by 0.315995
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.126
ELB improved by 0.29216
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.857
ELB improved by 0.268623
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.611
ELB improved by 0.246619
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.384
ELB improved by 0.226819
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.174
ELB improved by 0.209769
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.978
ELB improved by 0.196378
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.789
ELB improved by 0.188857
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.596
ELB improved by 0.193027
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.372
ELB improved by 0.223886
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.063
ELB improved by 0.30956
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.627
ELB improved by 0.435153
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.177
ELB improved by 0.450913
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.828
ELB improved by 0.348455
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.57
ELB improved by 0.258539
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.361
ELB improved by 0.20867
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.165
ELB improved by 0.195978
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.927
ELB improved by 0.238103
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.564
ELB improved by 0.362788
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.146
ELB improved by 0.417475
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.905
ELB improved by 0.241217
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.782
ELB improved by 0.123142
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.696
ELB improved by 0.0861981
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.628
ELB improved by 0.0678051
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.573
ELB improved by 0.0549337
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.528
ELB improved by 0.045273
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.49
ELB improved by 0.0378933
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.458
ELB improved by 0.0321804
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.43
ELB improved by 0.0276903
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.406
ELB improved by 0.0241039
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.385
ELB improved by 0.021194
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.366
ELB improved by 0.018798
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.349
ELB improved by 0.0167988
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.334
ELB improved by 0.0151108
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.32
ELB improved by 0.0136705
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.308
ELB improved by 0.0124305
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.297
ELB improved by 0.0113546
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.286
ELB improved by 0.0104148
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.277
ELB improved by 0.00958912
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-890.293
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.005
ELB improved by 312.288
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.799
ELB improved by 63.2067
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.07
ELB improved by 38.7286
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.596
ELB improved by 17.4742
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.893
ELB improved by 8.70248
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.549
ELB improved by 6.34398
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.335
ELB improved by 6.21468
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.71
ELB improved by 6.62517
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.181
ELB improved by 6.52834
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.644
ELB improved by 5.53743
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.416
ELB improved by 4.22805
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.184
ELB improved by 3.2318
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.69
ELB improved by 2.49418
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.82
ELB improved by 1.87
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.364
ELB improved by 1.45536
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.145
ELB improved by 1.21988
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.149
ELB improved by 0.995561
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.353
ELB improved by 0.796442
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.654
ELB improved by 0.698242
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.971
ELB improved by 0.682919
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.253
ELB improved by 0.71838
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.464
ELB improved by 0.789387
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.572
ELB improved by 0.891895
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.544
ELB improved by 1.02765
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.342
ELB improved by 1.20168
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.922
ELB improved by 1.42036
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.235
ELB improved by 1.68708
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.244
ELB improved by 1.99142
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.953
ELB improved by 2.29003
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.455
ELB improved by 2.49803
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.921
ELB improved by 2.53448
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.539
ELB improved by 2.38226
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.507
ELB improved by 2.0318
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.97
ELB improved by 1.53665
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.872
ELB improved by 1.09781
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.057
ELB improved by 0.815196
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.395
ELB improved by 0.662176
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.832
ELB improved by 0.563384
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.365
ELB improved by 0.466941
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.975
ELB improved by 0.3897
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.643
ELB improved by 0.332205
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.376
ELB improved by 0.266544
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.181
ELB improved by 0.195213
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.042
ELB improved by 0.139105
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.939
ELB improved by 0.102582
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.86
ELB improved by 0.0793665
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.796
ELB improved by 0.0636582
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.744
ELB improved by 0.0521858
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.701
ELB improved by 0.0433394
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.665
ELB improved by 0.0363177
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.634
ELB improved by 0.0306705
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.608
ELB improved by 0.0261005
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.585
ELB improved by 0.0223875
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.566
ELB improved by 0.0193594
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.549
ELB improved by 0.0168796
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.534
ELB improved by 0.0148398
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.521
ELB improved by 0.0131542
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.509
ELB improved by 0.0117548
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.499
ELB improved by 0.0105878
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.489
ELB improved by 0.00961032
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-835.153
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-583.417
ELB improved by 251.736
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-527.229
ELB improved by 56.1875
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.133
ELB improved by 43.0958
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.681
ELB improved by 22.4519
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.143
ELB improved by 9.53882
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.858
ELB improved by 5.28475
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.491
ELB improved by 4.3665
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.057
ELB improved by 4.43434
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.21
ELB improved by 4.84647
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.851
ELB improved by 5.35904
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.193
ELB improved by 5.658
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.812
ELB improved by 5.38149
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.333
ELB improved by 4.47888
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.046
ELB improved by 3.28709
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.826
ELB improved by 2.21997
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.361
ELB improved by 1.46509
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.377
ELB improved by 0.983607
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.693
ELB improved by 0.684495
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.194
ELB improved by 0.49862
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.813
ELB improved by 0.380926
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.51
ELB improved by 0.30334
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.26
ELB improved by 0.249447
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.05
ELB improved by 0.210082
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.87
ELB improved by 0.180135
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.714
ELB improved by 0.156656
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.576
ELB improved by 0.137838
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.453
ELB improved by 0.12251
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.343
ELB improved by 0.109865
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.244
ELB improved by 0.0993269
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.154
ELB improved by 0.0904708
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.071
ELB improved by 0.0829735
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.994
ELB improved by 0.0765858
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.923
ELB improved by 0.0711123
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.857
ELB improved by 0.0663973
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.794
ELB improved by 0.0623157
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.735
ELB improved by 0.0587653
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.68
ELB improved by 0.0556625
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.627
ELB improved by 0.0529377
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.576
ELB improved by 0.0505327
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.528
ELB improved by 0.0483986
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.481
ELB improved by 0.0464942
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.437
ELB improved by 0.0447842
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.393
ELB improved by 0.0432388
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.352
ELB improved by 0.0418327
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.311
ELB improved by 0.0405442
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.272
ELB improved by 0.0393549
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.233
ELB improved by 0.0382495
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.196
ELB improved by 0.0372151
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.16
ELB improved by 0.036241
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.125
ELB improved by 0.0353186
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.09
ELB improved by 0.0344408
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.057
ELB improved by 0.0336023
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.024
ELB improved by 0.0327991
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.992
ELB improved by 0.0320282
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.961
ELB improved by 0.0312877
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.93
ELB improved by 0.0305767
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.9
ELB improved by 0.0298946
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.871
ELB improved by 0.0292418
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.842
ELB improved by 0.0286189
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.814
ELB improved by 0.0280267
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.787
ELB improved by 0.0274664
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.76
ELB improved by 0.0269394
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.733
ELB improved by 0.0264469
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.707
ELB improved by 0.0259904
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.682
ELB improved by 0.0255712
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.657
ELB improved by 0.0251904
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.632
ELB improved by 0.0248492
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.607
ELB improved by 0.0245487
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.583
ELB improved by 0.0242895
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.559
ELB improved by 0.0240726
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.535
ELB improved by 0.0238983
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.511
ELB improved by 0.0237672
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.487
ELB improved by 0.0236794
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.464
ELB improved by 0.023635
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.44
ELB improved by 0.023634
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.416
ELB improved by 0.023676
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.393
ELB improved by 0.0237606
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.369
ELB improved by 0.0238869
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.345
ELB improved by 0.0240538
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.321
ELB improved by 0.02426
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.296
ELB improved by 0.0245032
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.271
ELB improved by 0.0247807
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.246
ELB improved by 0.0250886
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.221
ELB improved by 0.0254219
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.195
ELB improved by 0.0257735
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.169
ELB improved by 0.026134
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.142
ELB improved by 0.0264915
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.116
ELB improved by 0.0268305
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.088
ELB improved by 0.027132
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.061
ELB improved by 0.0273743
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.033
ELB improved by 0.0275336
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.006
ELB improved by 0.0275866
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.978
ELB improved by 0.0275132
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.951
ELB improved by 0.0272991
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.924
ELB improved by 0.0269388
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.898
ELB improved by 0.0264362
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.872
ELB improved by 0.0258037
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.847
ELB improved by 0.0250597
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.823
ELB improved by 0.0242259
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.799
ELB improved by 0.023324
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.777
ELB improved by 0.022374
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.756
ELB improved by 0.0213933
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.735
ELB improved by 0.0203963
iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.716
ELB improved by 0.0193951
iteration 106
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.697
ELB improved by 0.0183997
iteration 107
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.68
ELB improved by 0.0174186
iteration 108
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.663
ELB improved by 0.0164591
iteration 109
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.648
ELB improved by 0.0155272
iteration 110
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.633
ELB improved by 0.0146282
iteration 111
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.62
ELB improved by 0.0137664
iteration 112
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.607
ELB improved by 0.0129454
iteration 113
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.594
ELB improved by 0.0121681
iteration 114
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.583
ELB improved by 0.0114366
iteration 115
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.572
ELB improved by 0.0107528
iteration 116
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.562
ELB improved by 0.0101176
iteration 117
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.553
ELB improved by 0.00953209
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-886.849
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.816
ELB improved by 325.033
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.292
ELB improved by 57.525
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.199
ELB improved by 29.093
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.025
ELB improved by 12.1733
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.44
ELB improved by 6.58542
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.086
ELB improved by 5.35368
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.529
ELB improved by 5.55745
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.271
ELB improved by 6.25763
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.268
ELB improved by 7.00336
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.08
ELB improved by 7.18814
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.671
ELB improved by 6.40895
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.61
ELB improved by 5.0601
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.906
ELB improved by 3.70408
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.346
ELB improved by 2.5599
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.638
ELB improved by 1.70802
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.5
ELB improved by 1.13878
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.714
ELB improved by 0.785469
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.14
ELB improved by 0.574222
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.693
ELB improved by 0.447425
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.325
ELB improved by 0.367183
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.014
ELB improved by 0.311062
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.747
ELB improved by 0.267339
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.516
ELB improved by 0.230683
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.318
ELB improved by 0.198036
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.151
ELB improved by 0.167037
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.014
ELB improved by 0.13742
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.903
ELB improved by 0.111298
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.812
ELB improved by 0.0906353
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.736
ELB improved by 0.0754304
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.672
ELB improved by 0.0643586
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.616
ELB improved by 0.0560039
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.567
ELB improved by 0.0493823
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.523
ELB improved by 0.0439188
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.483
ELB improved by 0.0392895
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.448
ELB improved by 0.0353023
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.416
ELB improved by 0.0318327
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.388
ELB improved by 0.028792
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.361
ELB improved by 0.0261134
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.338
ELB improved by 0.023744
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.316
ELB improved by 0.0216409
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.296
ELB improved by 0.0197688
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.278
ELB improved by 0.0180981
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.262
ELB improved by 0.0166039
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.246
ELB improved by 0.0152649
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.232
ELB improved by 0.0140629
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.219
ELB improved by 0.0129821
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.207
ELB improved by 0.0120089
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.196
ELB improved by 0.0111315
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.186
ELB improved by 0.0103395
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.176
ELB improved by 0.00962388
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.804 0.202 2.999
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.048 | 0.004 | 0.053 | |
| getPIPs | 0.041 | 0.005 | 0.047 | |
| graper | 0.073 | 0.000 | 0.073 | |
| makeExampleData | 0.008 | 0.000 | 0.008 | |
| makeExampleDataWithUnequalGroups | 0.010 | 0.000 | 0.009 | |
| plotELBO | 0.412 | 0.012 | 0.424 | |
| plotGroupPenalties | 1.470 | 0.060 | 1.534 | |
| plotPosterior | 0.961 | 0.012 | 0.976 | |
| predict.graper | 1.001 | 0.028 | 1.032 | |
| print.graper | 0.045 | 0.004 | 0.049 | |