Britta Velten
| Snapshot Date: 2025-12-01 13:40 -0500 (Mon, 01 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 95474d7 |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-02 11:35 -0500 (Tue, 02 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4572 |
| 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 913/2328 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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. |
| Package: graper |
| Version: 1.27.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz |
| StartedAt: 2025-12-02 00:15:27 -0500 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 00:17:00 -0500 (Tue, 02 Dec 2025) |
| EllapsedTime: 92.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* 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 ... INFO
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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-bioc/R/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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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=-862.626
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-593.521
ELB improved by 269.106
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-535.437
ELB improved by 58.0837
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-493.847
ELB improved by 41.5903
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.748
ELB improved by 22.0985
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.585
ELB improved by 10.1632
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.877
ELB improved by 5.70873
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.509
ELB improved by 4.36793
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.623
ELB improved by 3.8853
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.899
ELB improved by 3.72424
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.223
ELB improved by 3.67641
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.582
ELB improved by 3.64092
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.055
ELB improved by 3.52707
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.812
ELB improved by 3.24311
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.05
ELB improved by 2.76134
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.882
ELB improved by 2.16817
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.28
ELB improved by 1.60162
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.131
ELB improved by 1.1493
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.306
ELB improved by 0.82532
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.7
ELB improved by 0.605862
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.24
ELB improved by 0.460169
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.877
ELB improved by 0.362641
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.582
ELB improved by 0.295423
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.334
ELB improved by 0.247345
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.123
ELB improved by 0.211766
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.938
ELB improved by 0.184723
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.774
ELB improved by 0.163774
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.627
ELB improved by 0.147348
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.492
ELB improved by 0.1344
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.368
ELB improved by 0.124216
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.252
ELB improved by 0.116302
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.141
ELB improved by 0.110314
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.035
ELB improved by 0.106014
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.932
ELB improved by 0.103249
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.83
ELB improved by 0.101927
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.728
ELB improved by 0.102013
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.625
ELB improved by 0.103525
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.518
ELB improved by 0.106529
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.407
ELB improved by 0.111142
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.29
ELB improved by 0.11754
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.164
ELB improved by 0.125955
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.027
ELB improved by 0.136688
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.877
ELB improved by 0.150112
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.71
ELB improved by 0.166675
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.523
ELB improved by 0.186897
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.312
ELB improved by 0.21136
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.071
ELB improved by 0.240676
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.796
ELB improved by 0.275434
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.48
ELB improved by 0.316099
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.117
ELB improved by 0.36286
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.701
ELB improved by 0.415389
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.229
ELB improved by 0.4725
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.697
ELB improved by 0.531739
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.108
ELB improved by 0.589004
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.47
ELB improved by 0.63848
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.796
ELB improved by 0.673219
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.11
ELB improved by 0.686551
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.436
ELB improved by 0.673986
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.801
ELB improved by 0.634781
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.229
ELB improved by 0.572598
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.733
ELB improved by 0.495081
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.321
ELB improved by 0.412052
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.989
ELB improved by 0.332597
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.726
ELB improved by 0.262714
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.521
ELB improved by 0.204853
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.362
ELB improved by 0.158866
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.239
ELB improved by 0.123256
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.143
ELB improved by 0.0960888
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.068
ELB improved by 0.0754988
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.008
ELB improved by 0.0598995
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.96
ELB improved by 0.0480338
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.921
ELB improved by 0.0389457
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.889
ELB improved by 0.031926
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.862
ELB improved by 0.0264544
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.84
ELB improved by 0.0221504
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.821
ELB improved by 0.0187353
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.805
ELB improved by 0.0160032
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.792
ELB improved by 0.0138006
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.78
ELB improved by 0.0120124
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.769
ELB improved by 0.0105507
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.76
ELB improved by 0.00934826
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-817.706
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.751
ELB improved by 235.955
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-520.597
ELB improved by 61.1546
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.314
ELB improved by 51.2824
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.258
ELB improved by 27.0563
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.437
ELB improved by 9.82117
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.997
ELB improved by 4.43951
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.174
ELB improved by 2.8227
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.952
ELB improved by 2.22222
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.97
ELB improved by 1.98179
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.058
ELB improved by 1.91217
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.12
ELB improved by 1.93837
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.094
ELB improved by 2.02616
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.946
ELB improved by 2.14736
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.689
ELB improved by 2.25741
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.401
ELB improved by 2.2877
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.231
ELB improved by 2.1704
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.34
ELB improved by 1.89118
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.827
ELB improved by 1.51296
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.689
ELB improved by 1.13726
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.847
ELB improved by 0.842076
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.199
ELB improved by 0.648087
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.667
ELB improved by 0.532443
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.206
ELB improved by 0.46133
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.793
ELB improved by 0.4127
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.413
ELB improved by 0.379934
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.051
ELB improved by 0.361606
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.696
ELB improved by 0.354951
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.34
ELB improved by 0.356503
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.976
ELB improved by 0.363504
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.602
ELB improved by 0.374194
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.214
ELB improved by 0.38766
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.811
ELB improved by 0.403636
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.389
ELB improved by 0.422284
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.945
ELB improved by 0.4439
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.476
ELB improved by 0.468555
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.98
ELB improved by 0.495677
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.457
ELB improved by 0.523642
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.907
ELB improved by 0.549511
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.338
ELB improved by 0.569243
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.759
ELB improved by 0.578758
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.184
ELB improved by 0.575594
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.624
ELB improved by 0.560122
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.088
ELB improved by 0.535583
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.581
ELB improved by 0.507307
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.099
ELB improved by 0.481147
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.64
ELB improved by 0.459313
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.208
ELB improved by 0.432374
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.827
ELB improved by 0.380756
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.524
ELB improved by 0.303387
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.297
ELB improved by 0.226314
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.129
ELB improved by 0.167874
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.002
ELB improved by 0.127835
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.901
ELB improved by 0.100306
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.821
ELB improved by 0.0806698
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.755
ELB improved by 0.0661585
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.699
ELB improved by 0.0551403
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.653
ELB improved by 0.0465978
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.613
ELB improved by 0.0398597
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.578
ELB improved by 0.0344648
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.548
ELB improved by 0.0300873
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.522
ELB improved by 0.0264919
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.498
ELB improved by 0.0235065
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.477
ELB improved by 0.0210025
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.458
ELB improved by 0.0188831
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.441
ELB improved by 0.0170743
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.426
ELB improved by 0.0155187
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.412
ELB improved by 0.0141714
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.399
ELB improved by 0.012997
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.387
ELB improved by 0.0119672
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.376
ELB improved by 0.0110592
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.365
ELB improved by 0.0102546
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.356
ELB improved by 0.00953823
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-863.721
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-574.451
ELB improved by 289.27
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.754
ELB improved by 56.6967
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.944
ELB improved by 37.8102
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.944
ELB improved by 19.0006
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.162
ELB improved by 9.78162
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.434
ELB improved by 5.7278
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.367
ELB improved by 4.06706
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.773
ELB improved by 3.59442
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.282
ELB improved by 3.49103
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.913
ELB improved by 3.36887
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.86
ELB improved by 3.05249
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.324
ELB improved by 2.53642
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.379
ELB improved by 1.94462
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.969
ELB improved by 1.41004
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.968
ELB improved by 1.00092
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.24
ELB improved by 0.728083
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.674
ELB improved by 0.566451
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.197
ELB improved by 0.477069
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.768
ELB improved by 0.428481
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.367
ELB improved by 0.401775
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.98
ELB improved by 0.386384
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.604
ELB improved by 0.376204
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.236
ELB improved by 0.367689
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.877
ELB improved by 0.359157
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.527
ELB improved by 0.350523
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.184
ELB improved by 0.342879
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.846
ELB improved by 0.337214
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.515
ELB improved by 0.331819
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.194
ELB improved by 0.320575
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.896
ELB improved by 0.297852
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.63
ELB improved by 0.266488
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.395
ELB improved by 0.23463
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.188
ELB improved by 0.207144
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.003
ELB improved by 0.184663
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.837
ELB improved by 0.166381
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.685
ELB improved by 0.151481
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.546
ELB improved by 0.139356
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.417
ELB improved by 0.129563
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.295
ELB improved by 0.121767
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.179
ELB improved by 0.115725
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.068
ELB improved by 0.111275
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.959
ELB improved by 0.108342
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.852
ELB improved by 0.106942
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.745
ELB improved by 0.107199
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.636
ELB improved by 0.109356
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.522
ELB improved by 0.113764
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.401
ELB improved by 0.120777
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.271
ELB improved by 0.130427
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.129
ELB improved by 0.141828
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.976
ELB improved by 0.152667
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.817
ELB improved by 0.159848
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.655
ELB improved by 0.161599
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.496
ELB improved by 0.158807
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.342
ELB improved by 0.153774
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.194
ELB improved by 0.14827
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.051
ELB improved by 0.142924
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.914
ELB improved by 0.137589
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.782
ELB improved by 0.13182
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.657
ELB improved by 0.125189
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.539
ELB improved by 0.11745
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.431
ELB improved by 0.108596
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.332
ELB improved by 0.0988348
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.243
ELB improved by 0.0885205
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.165
ELB improved by 0.0780704
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.097
ELB improved by 0.0678888
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.039
ELB improved by 0.0583126
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.989
ELB improved by 0.0495804
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.948
ELB improved by 0.0418264
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.912
ELB improved by 0.0350923
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.883
ELB improved by 0.0293489
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.859
ELB improved by 0.0245204
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.838
ELB improved by 0.020506
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.821
ELB improved by 0.0171957
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.806
ELB improved by 0.0144819
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.794
ELB improved by 0.0122654
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.784
ELB improved by 0.0104586
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.775
ELB improved by 0.00898652
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-901.956
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-589.357
ELB improved by 312.599
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-530.608
ELB improved by 58.7491
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.287
ELB improved by 40.3208
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.497
ELB improved by 18.7906
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.939
ELB improved by 7.55797
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.621
ELB improved by 4.31772
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.027
ELB improved by 3.5943
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.506
ELB improved by 3.52048
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.771
ELB improved by 3.73546
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.648
ELB improved by 4.12312
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.091
ELB improved by 4.55661
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.313
ELB improved by 4.77802
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.834
ELB improved by 4.47885
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.205
ELB improved by 3.62901
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.623
ELB improved by 2.58182
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.924
ELB improved by 1.69902
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.823
ELB improved by 1.10123
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.079
ELB improved by 0.744091
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.539
ELB improved by 0.540402
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.117
ELB improved by 0.421765
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.768
ELB improved by 0.348657
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.467
ELB improved by 0.300843
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.199
ELB improved by 0.268178
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.954
ELB improved by 0.24544
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.724
ELB improved by 0.229816
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.504
ELB improved by 0.21973
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.29
ELB improved by 0.214285
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.077
ELB improved by 0.212988
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.861
ELB improved by 0.215593
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.639
ELB improved by 0.221993
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.407
ELB improved by 0.232108
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.162
ELB improved by 0.245752
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.899
ELB improved by 0.262474
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.618
ELB improved by 0.281413
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.316
ELB improved by 0.301282
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.996
ELB improved by 0.320559
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.658
ELB improved by 0.337843
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.306
ELB improved by 0.352212
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.942
ELB improved by 0.363391
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.571
ELB improved by 0.371727
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.193
ELB improved by 0.378028
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.809
ELB improved by 0.383371
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.42
ELB improved by 0.38893
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.024
ELB improved by 0.395844
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.619
ELB improved by 0.4051
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.202
ELB improved by 0.417314
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.77
ELB improved by 0.432392
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.32
ELB improved by 0.449193
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.855
ELB improved by 0.465456
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.377
ELB improved by 0.478124
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.893
ELB improved by 0.483831
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.414
ELB improved by 0.479442
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.95
ELB improved by 0.46324
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.513
ELB improved by 0.436902
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.106
ELB improved by 0.407161
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.719
ELB improved by 0.387652
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.312
ELB improved by 0.406966
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.779
ELB improved by 0.533071
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.942
ELB improved by 0.836193
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.839
ELB improved by 1.10314
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.72
ELB improved by 1.11969
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.808
ELB improved by 0.911364
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.15
ELB improved by 0.658356
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.701
ELB improved by 0.449082
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.411
ELB improved by 0.28937
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.229
ELB improved by 0.182589
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.111
ELB improved by 0.118218
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.03
ELB improved by 0.0810397
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.97
ELB improved by 0.0592892
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.925
ELB improved by 0.0457261
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.888
ELB improved by 0.0364402
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.859
ELB improved by 0.0295192
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.834
ELB improved by 0.0240973
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.815
ELB improved by 0.0197864
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.798
ELB improved by 0.0163789
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.785
ELB improved by 0.0137203
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.773
ELB improved by 0.0116702
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.763
ELB improved by 0.0100994
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.754
ELB improved by 0.00889619
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.487 0.235 2.711
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.054 | 0.012 | 0.066 | |
| getPIPs | 0.044 | 0.017 | 0.062 | |
| graper | 0.077 | 0.023 | 0.100 | |
| makeExampleData | 0.008 | 0.003 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.000 | 0.013 | |
| plotELBO | 0.315 | 0.025 | 0.340 | |
| plotGroupPenalties | 1.133 | 0.051 | 1.187 | |
| plotPosterior | 0.646 | 0.018 | 0.668 | |
| predict.graper | 2.044 | 0.072 | 2.117 | |
| print.graper | 0.050 | 0.013 | 0.064 | |