Britta Velten
| Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 Oct 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 2025-10-04 12:07 -0400 (Sat, 04 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" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| 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 915/2341 | 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: 2025-10-03 07:46:47 -0000 (Fri, 03 Oct 2025) |
| EndedAt: 2025-10-03 07:48:01 -0000 (Fri, 03 Oct 2025) |
| EllapsedTime: 74.1 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=-871.279
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.599
ELB improved by 290.68
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.321
ELB improved by 63.2783
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.65
ELB improved by 42.6713
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.596
ELB improved by 19.0538
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.324
ELB improved by 8.27248
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.951
ELB improved by 5.37274
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.057
ELB improved by 4.89402
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.918
ELB improved by 5.13837
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.385
ELB improved by 5.53328
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.751
ELB improved by 5.63402
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.714
ELB improved by 5.03755
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.827
ELB improved by 3.88669
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.006
ELB improved by 2.82136
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.851
ELB improved by 2.155
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.038
ELB improved by 1.81292
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.393
ELB improved by 1.6448
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.84
ELB improved by 1.55282
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.35
ELB improved by 1.4905
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.91
ELB improved by 1.43928
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.519
ELB improved by 1.39158
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.177
ELB improved by 1.34157
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.896
ELB improved by 1.28134
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.694
ELB improved by 1.20159
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.598
ELB improved by 1.09592
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.633
ELB improved by 0.965621
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.812
ELB improved by 0.820983
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.134
ELB improved by 0.67786
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.582
ELB improved by 0.551867
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.129
ELB improved by 0.453345
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.743
ELB improved by 0.385214
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.4
ELB improved by 0.343766
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.078
ELB improved by 0.321225
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.768
ELB improved by 0.310605
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.455
ELB improved by 0.312563
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.125
ELB improved by 0.330524
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.789
ELB improved by 0.33552
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.518
ELB improved by 0.271652
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.349
ELB improved by 0.168603
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.253
ELB improved by 0.0958236
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.194
ELB improved by 0.0590096
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.154
ELB improved by 0.0405397
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.123
ELB improved by 0.030084
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.1
ELB improved by 0.0234319
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.081
ELB improved by 0.0188513
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.066
ELB improved by 0.0155366
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.053
ELB improved by 0.0130581
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.041
ELB improved by 0.0111601
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.032
ELB improved by 0.00967856
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-896.265
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-587.295
ELB improved by 308.971
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.471
ELB improved by 61.8234
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.375
ELB improved by 41.0966
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.888
ELB improved by 18.4871
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.562
ELB improved by 7.32563
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.417
ELB improved by 4.14546
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.121
ELB improved by 3.29598
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.128
ELB improved by 2.99275
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.271
ELB improved by 2.85702
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.51
ELB improved by 2.76075
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.864
ELB improved by 2.64572
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.386
ELB improved by 2.47818
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.147
ELB improved by 2.23911
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.212
ELB improved by 1.93505
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.603
ELB improved by 1.60899
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.278
ELB improved by 1.32491
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.15
ELB improved by 1.12841
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.142
ELB improved by 1.00801
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.234
ELB improved by 0.907971
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.428
ELB improved by 0.805696
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.719
ELB improved by 0.709477
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.102
ELB improved by 0.61658
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.572
ELB improved by 0.529559
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.113
ELB improved by 0.459084
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.706
ELB improved by 0.406837
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.342
ELB improved by 0.364179
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.022
ELB improved by 0.319929
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.753
ELB improved by 0.269376
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.535
ELB improved by 0.218055
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.361
ELB improved by 0.174267
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.219
ELB improved by 0.141208
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.102
ELB improved by 0.117347
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.002
ELB improved by 0.0998734
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.916
ELB improved by 0.0865367
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.84
ELB improved by 0.0759154
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.773
ELB improved by 0.0671764
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.713
ELB improved by 0.0598251
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.659
ELB improved by 0.0535498
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.611
ELB improved by 0.0481383
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.568
ELB improved by 0.0434367
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.528
ELB improved by 0.0393277
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.493
ELB improved by 0.0357187
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.46
ELB improved by 0.0325354
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.43
ELB improved by 0.0297169
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.403
ELB improved by 0.027213
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.378
ELB improved by 0.0249817
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.355
ELB improved by 0.0229878
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.334
ELB improved by 0.0212014
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.314
ELB improved by 0.0195973
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.296
ELB improved by 0.0181536
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.279
ELB improved by 0.0168516
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.264
ELB improved by 0.0156753
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.249
ELB improved by 0.0146107
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.235
ELB improved by 0.0136455
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.223
ELB improved by 0.012769
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.211
ELB improved by 0.0119721
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.199
ELB improved by 0.0112463
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.189
ELB improved by 0.0105846
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.179
ELB improved by 0.00998048
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-873.928
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-604.19
ELB improved by 269.738
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-544.251
ELB improved by 59.9394
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.622
ELB improved by 48.6286
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.822
ELB improved by 25.7995
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.034
ELB improved by 10.7884
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.225
ELB improved by 5.80878
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.449
ELB improved by 4.77579
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.766
ELB improved by 4.68376
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.985
ELB improved by 4.78077
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.299
ELB improved by 4.68625
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.139
ELB improved by 4.15939
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.885
ELB improved by 3.25389
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.589
ELB improved by 2.29619
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.03
ELB improved by 1.5587
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.942
ELB improved by 1.08833
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.137
ELB improved by 0.804732
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.523
ELB improved by 0.614295
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.058
ELB improved by 0.465209
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.708
ELB improved by 0.349582
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.44
ELB improved by 0.268054
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.227
ELB improved by 0.213407
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.051
ELB improved by 0.176374
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.9
ELB improved by 0.150213
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.769
ELB improved by 0.130868
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.653
ELB improved by 0.116017
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.549
ELB improved by 0.10431
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.454
ELB improved by 0.0949179
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.367
ELB improved by 0.0873015
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.286
ELB improved by 0.0810828
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.21
ELB improved by 0.0759841
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.138
ELB improved by 0.0717932
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.07
ELB improved by 0.0683455
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.004
ELB improved by 0.0655119
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.941
ELB improved by 0.0631914
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.88
ELB improved by 0.0613059
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.82
ELB improved by 0.059795
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.761
ELB improved by 0.0586138
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.704
ELB improved by 0.0577291
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.646
ELB improved by 0.057118
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.59
ELB improved by 0.0567663
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.533
ELB improved by 0.056667
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.476
ELB improved by 0.0568201
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.419
ELB improved by 0.0572314
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.361
ELB improved by 0.0579128
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.302
ELB improved by 0.058882
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.242
ELB improved by 0.060163
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.18
ELB improved by 0.0617859
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.116
ELB improved by 0.063788
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.05
ELB improved by 0.0662142
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.981
ELB improved by 0.069118
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.909
ELB improved by 0.0725632
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.832
ELB improved by 0.0766246
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.75
ELB improved by 0.0813908
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.664
ELB improved by 0.0869665
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.57
ELB improved by 0.0934765
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.469
ELB improved by 0.101071
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.359
ELB improved by 0.109935
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.239
ELB improved by 0.120301
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.106
ELB improved by 0.132477
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.959
ELB improved by 0.146893
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.795
ELB improved by 0.164189
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.61
ELB improved by 0.185404
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.397
ELB improved by 0.212364
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.149
ELB improved by 0.248527
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.848
ELB improved by 0.300757
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.466
ELB improved by 0.382246
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.955
ELB improved by 0.51128
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.275
ELB improved by 0.679876
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.475
ELB improved by 0.799854
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.676
ELB improved by 0.799054
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.945
ELB improved by 0.730539
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.28
ELB improved by 0.665526
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.625
ELB improved by 0.654992
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.917
ELB improved by 0.707751
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.241
ELB improved by 0.675997
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.74
ELB improved by 0.501035
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.405
ELB improved by 0.334958
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.182
ELB improved by 0.223177
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.032
ELB improved by 0.150143
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.93
ELB improved by 0.102047
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.859
ELB improved by 0.0703646
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.81
ELB improved by 0.0495176
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.774
ELB improved by 0.035754
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.747
ELB improved by 0.0265924
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.727
ELB improved by 0.0204274
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.711
ELB improved by 0.0162312
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.697
ELB improved by 0.0133463
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.686
ELB improved by 0.01135
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.676
ELB improved by 0.00996968
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-848.812
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-591.358
ELB improved by 257.455
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-534.045
ELB improved by 57.3132
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.862
ELB improved by 47.1824
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.339
ELB improved by 29.5228
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.32
ELB improved by 14.0197
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.104
ELB improved by 6.21595
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.978
ELB improved by 4.12568
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.235
ELB improved by 3.74356
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.423
ELB improved by 3.81112
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.407
ELB improved by 4.01676
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.217
ELB improved by 4.18963
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.013
ELB improved by 4.20392
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.975
ELB improved by 4.03775
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.129
ELB improved by 3.84656
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.461
ELB improved by 3.66736
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.27
ELB improved by 3.19133
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.895
ELB improved by 2.37468
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.295
ELB improved by 1.60019
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.225
ELB improved by 1.07044
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.47
ELB improved by 0.754417
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.895
ELB improved by 0.575875
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.419
ELB improved by 0.475897
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.999
ELB improved by 0.419129
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.613
ELB improved by 0.386428
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.245
ELB improved by 0.367792
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.887
ELB improved by 0.358009
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.533
ELB improved by 0.354363
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.177
ELB improved by 0.355491
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.817
ELB improved by 0.360836
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.446
ELB improved by 0.370382
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.062
ELB improved by 0.384533
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.658
ELB improved by 0.404103
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.227
ELB improved by 0.430373
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.762
ELB improved by 0.465237
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.251
ELB improved by 0.511381
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.678
ELB improved by 0.572339
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.026
ELB improved by 0.652008
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.273
ELB improved by 0.752889
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.401
ELB improved by 0.872388
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.404
ELB improved by 0.996759
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.314
ELB improved by 1.09054
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.225
ELB improved by 1.0884
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.273
ELB improved by 0.952291
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.525
ELB improved by 0.747829
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.968
ELB improved by 0.556952
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.56
ELB improved by 0.408403
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.26
ELB improved by 0.300183
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.039
ELB improved by 0.220917
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.878
ELB improved by 0.160727
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.762
ELB improved by 0.115685
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.677
ELB improved by 0.0848692
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.611
ELB improved by 0.0661413
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.555
ELB improved by 0.0557704
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.506
ELB improved by 0.0498104
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.461
ELB improved by 0.0450146
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.421
ELB improved by 0.0394337
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.388
ELB improved by 0.0327484
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.363
ELB improved by 0.0258222
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.343
ELB improved by 0.0196953
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.328
ELB improved by 0.0149049
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.317
ELB improved by 0.0114553
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.308
ELB improved by 0.00908318
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.728 0.219 2.940
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.048 | 0.004 | 0.052 | |
| getPIPs | 0.047 | 0.000 | 0.046 | |
| graper | 0.073 | 0.000 | 0.074 | |
| makeExampleData | 0.008 | 0.000 | 0.009 | |
| makeExampleDataWithUnequalGroups | 0.009 | 0.000 | 0.010 | |
| plotELBO | 0.405 | 0.020 | 0.426 | |
| plotGroupPenalties | 1.473 | 0.072 | 1.547 | |
| plotPosterior | 0.935 | 0.008 | 0.944 | |
| predict.graper | 0.956 | 0.040 | 0.998 | |
| print.graper | 0.032 | 0.016 | 0.048 | |