Britta Velten
| Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 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 2025-09-29 12:03 -0400 (Mon, 29 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" | 4833 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4621 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4566 |
| 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. |
| Package: graper |
| Version: 1.25.2 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graper_1.25.2.tar.gz |
| StartedAt: 2025-09-29 00:32:48 -0400 (Mon, 29 Sep 2025) |
| EndedAt: 2025-09-29 00:34:19 -0400 (Mon, 29 Sep 2025) |
| EllapsedTime: 91.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graper_1.25.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.25.2’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.22-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.25.2’ ** 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-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-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 version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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=-844.822
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.805
ELB improved by 264.017
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.203
ELB improved by 63.6021
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.944
ELB improved by 45.2588
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.008
ELB improved by 19.9361
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.801
ELB improved by 7.20666
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.758
ELB improved by 4.04328
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.714
ELB improved by 3.04378
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.083
ELB improved by 2.63139
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.649
ELB improved by 2.43375
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.341
ELB improved by 2.30823
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.127
ELB improved by 2.21401
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.986
ELB improved by 2.14081
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.9
ELB improved by 2.08593
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.857
ELB improved by 2.04275
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.864
ELB improved by 1.99274
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.96
ELB improved by 1.90468
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.211
ELB improved by 1.74857
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.686
ELB improved by 1.52457
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.409
ELB improved by 1.27709
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.338
ELB improved by 1.07101
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.407
ELB improved by 0.931761
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.638
ELB improved by 0.768839
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.092
ELB improved by 0.545958
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.724
ELB improved by 0.367844
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.457
ELB improved by 0.267257
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.241
ELB improved by 0.215791
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.052
ELB improved by 0.188545
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.88
ELB improved by 0.172874
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.717
ELB improved by 0.162972
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.56
ELB improved by 0.156061
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.41
ELB improved by 0.150697
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.264
ELB improved by 0.146062
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.122
ELB improved by 0.141649
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.985
ELB improved by 0.137124
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.853
ELB improved by 0.132268
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.726
ELB improved by 0.126971
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.604
ELB improved by 0.121227
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.489
ELB improved by 0.115122
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.381
ELB improved by 0.108809
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.278
ELB improved by 0.10247
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.182
ELB improved by 0.0962791
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.091
ELB improved by 0.0903812
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.007
ELB improved by 0.0848872
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.927
ELB improved by 0.0798743
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.851
ELB improved by 0.0753938
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.78
ELB improved by 0.0714804
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.712
ELB improved by 0.0681619
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.646
ELB improved by 0.0654676
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.583
ELB improved by 0.0634363
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.521
ELB improved by 0.0621222
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.459
ELB improved by 0.0615962
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.397
ELB improved by 0.0619389
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.334
ELB improved by 0.0632143
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.268
ELB improved by 0.0654155
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.2
ELB improved by 0.0683788
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.128
ELB improved by 0.0717057
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.054
ELB improved by 0.0747868
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.977
ELB improved by 0.077015
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.898
ELB improved by 0.0781024
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.82
ELB improved by 0.0782158
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.742
ELB improved by 0.0777866
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.665
ELB improved by 0.0772035
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.589
ELB improved by 0.0766582
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.512
ELB improved by 0.0761708
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.437
ELB improved by 0.0756744
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.362
ELB improved by 0.0750777
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.287
ELB improved by 0.0742953
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.214
ELB improved by 0.0732587
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.142
ELB improved by 0.0719191
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.072
ELB improved by 0.07025
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.004
ELB improved by 0.0682478
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.938
ELB improved by 0.0659327
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.874
ELB improved by 0.063348
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.814
ELB improved by 0.0605598
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.756
ELB improved by 0.0576552
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.701
ELB improved by 0.0547419
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.649
ELB improved by 0.0519504
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.6
ELB improved by 0.0494385
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.553
ELB improved by 0.0474028
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.507
ELB improved by 0.0460937
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.461
ELB improved by 0.0458316
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.414
ELB improved by 0.047
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.364
ELB improved by 0.0499615
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.309
ELB improved by 0.0548101
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.248
ELB improved by 0.0609664
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.181
ELB improved by 0.0670151
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.109
ELB improved by 0.0714845
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.035
ELB improved by 0.0742042
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.959
ELB improved by 0.0764853
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.879
ELB improved by 0.0801192
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.791
ELB improved by 0.0873053
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.69
ELB improved by 0.101524
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.563
ELB improved by 0.126362
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.405
ELB improved by 0.158551
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.226
ELB improved by 0.178953
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.059
ELB improved by 0.167269
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.925
ELB improved by 0.133476
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.825
ELB improved by 0.100652
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.748
ELB improved by 0.0765772
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.689
ELB improved by 0.0591612
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.643
ELB improved by 0.0457766
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.608
ELB improved by 0.0352038
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.581
ELB improved by 0.0270017
iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.56
ELB improved by 0.0208633
iteration 106
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.544
ELB improved by 0.0164029
iteration 107
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.53
ELB improved by 0.013201
iteration 108
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.52
ELB improved by 0.0108901
iteration 109
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.51
ELB improved by 0.00919244
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-848.335
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-557.503
ELB improved by 290.832
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.815
ELB improved by 61.6878
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.668
ELB improved by 37.1468
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.583
ELB improved by 16.0854
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.11
ELB improved by 7.47321
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.61
ELB improved by 4.5
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.982
ELB improved by 3.62777
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.396
ELB improved by 3.58542
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.444
ELB improved by 3.95203
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.994
ELB improved by 4.45042
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.247
ELB improved by 4.74698
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.725
ELB improved by 4.52221
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.977
ELB improved by 3.74797
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.228
ELB improved by 2.74913
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.353
ELB improved by 1.87444
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.112
ELB improved by 1.24145
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.283
ELB improved by 0.829
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.702
ELB improved by 0.580754
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.268
ELB improved by 0.43439
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.923
ELB improved by 0.344533
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.638
ELB improved by 0.285546
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.393
ELB improved by 0.244171
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.18
ELB improved by 0.213477
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.99
ELB improved by 0.189642
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.82
ELB improved by 0.170425
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.665
ELB improved by 0.154442
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.525
ELB improved by 0.140801
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.396
ELB improved by 0.128912
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.277
ELB improved by 0.118374
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.168
ELB improved by 0.108909
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.068
ELB improved by 0.100326
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.976
ELB improved by 0.0924876
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.89
ELB improved by 0.085297
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.812
ELB improved by 0.0786826
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.739
ELB improved by 0.0725901
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.672
ELB improved by 0.0669766
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.61
ELB improved by 0.0618061
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.553
ELB improved by 0.057047
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.501
ELB improved by 0.0526704
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.452
ELB improved by 0.048649
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.407
ELB improved by 0.044957
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.365
ELB improved by 0.0415694
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.327
ELB improved by 0.0384625
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.291
ELB improved by 0.0356136
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.258
ELB improved by 0.0330015
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.228
ELB improved by 0.0306059
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.199
ELB improved by 0.0284083
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.173
ELB improved by 0.0263914
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.148
ELB improved by 0.0245392
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.126
ELB improved by 0.0228371
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.104
ELB improved by 0.021272
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.084
ELB improved by 0.0198317
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.066
ELB improved by 0.0185052
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.049
ELB improved by 0.0172825
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.032
ELB improved by 0.0161546
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.017
ELB improved by 0.0151134
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.003
ELB improved by 0.0141514
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.99
ELB improved by 0.0132619
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.978
ELB improved by 0.0124389
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.966
ELB improved by 0.0116768
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.955
ELB improved by 0.0109706
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.945
ELB improved by 0.0103157
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.935
ELB improved by 0.009708
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-821.537
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-547.269
ELB improved by 274.268
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.526
ELB improved by 55.7432
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.222
ELB improved by 30.3037
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.447
ELB improved by 11.775
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.288
ELB improved by 5.15922
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.194
ELB improved by 3.09364
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.723
ELB improved by 2.47074
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.425
ELB improved by 2.29791
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.161
ELB improved by 2.26409
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.899
ELB improved by 2.26265
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.654
ELB improved by 2.2446
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.476
ELB improved by 2.17827
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.429
ELB improved by 2.04678
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.575
ELB improved by 1.85422
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.963
ELB improved by 1.61224
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.641
ELB improved by 1.32202
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.628
ELB improved by 1.01286
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.878
ELB improved by 0.750006
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.309
ELB improved by 0.568393
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.849
ELB improved by 0.4601
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.447
ELB improved by 0.402088
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.079
ELB improved by 0.368015
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.747
ELB improved by 0.331659
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.462
ELB improved by 0.284991
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.219
ELB improved by 0.243666
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416
ELB improved by 0.218985
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.792
ELB improved by 0.208186
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.586
ELB improved by 0.205439
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.379
ELB improved by 0.207089
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.168
ELB improved by 0.211355
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.95
ELB improved by 0.217396
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.726
ELB improved by 0.22481
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.492
ELB improved by 0.233434
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.249
ELB improved by 0.243296
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.994
ELB improved by 0.254617
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.726
ELB improved by 0.267851
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.443
ELB improved by 0.283726
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.139
ELB improved by 0.303279
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.811
ELB improved by 0.327893
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.452
ELB improved by 0.359305
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.053
ELB improved by 0.399578
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.602
ELB improved by 0.450967
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.086
ELB improved by 0.515604
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.491
ELB improved by 0.594901
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.803
ELB improved by 0.688593
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.009
ELB improved by 0.793438
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.108
ELB improved by 0.901502
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.11
ELB improved by 0.997738
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.053
ELB improved by 1.05635
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.013
ELB improved by 1.04004
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.089
ELB improved by 0.924083
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.348
ELB improved by 0.741679
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.787
ELB improved by 0.560853
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.37
ELB improved by 0.416901
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.061
ELB improved by 0.308648
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.835
ELB improved by 0.226234
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.671
ELB improved by 0.163759
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.553
ELB improved by 0.118087
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.467
ELB improved by 0.0859195
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.404
ELB improved by 0.0636833
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.355
ELB improved by 0.0483301
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.318
ELB improved by 0.0376311
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.288
ELB improved by 0.0300651
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.263
ELB improved by 0.0246182
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.242
ELB improved by 0.0206176
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.225
ELB improved by 0.0176155
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.209
ELB improved by 0.0153126
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.196
ELB improved by 0.0135067
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.184
ELB improved by 0.0120601
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.173
ELB improved by 0.0108779
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.163
ELB improved by 0.00989386
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.295
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-595.998
ELB improved by 260.297
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-535.811
ELB improved by 60.1864
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.351
ELB improved by 50.4604
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.504
ELB improved by 26.8473
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.692
ELB improved by 9.81189
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.379
ELB improved by 4.3127
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.552
ELB improved by 2.82673
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.195
ELB improved by 2.35743
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.905
ELB improved by 2.28987
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.508
ELB improved by 2.39709
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.932
ELB improved by 2.57622
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.195
ELB improved by 2.73646
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.432
ELB improved by 2.7635
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.87
ELB improved by 2.56165
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.724
ELB improved by 2.14572
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.067
ELB improved by 1.65777
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.816
ELB improved by 1.25073
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.832
ELB improved by 0.983695
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417
ELB improved by 0.83228
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.249
ELB improved by 0.750639
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.539
ELB improved by 0.709762
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.843
ELB improved by 0.69624
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.144
ELB improved by 0.699164
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.437
ELB improved by 0.706816
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.727
ELB improved by 0.710115
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.02
ELB improved by 0.706661
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.32
ELB improved by 0.700636
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.621
ELB improved by 0.698709
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.914
ELB improved by 0.706997
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.184
ELB improved by 0.730302
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.413
ELB improved by 0.770281
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.594
ELB improved by 0.819248
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.737
ELB improved by 0.857036
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.867
ELB improved by 0.870046
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.996
ELB improved by 0.871548
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.098
ELB improved by 0.897409
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.096
ELB improved by 1.00227
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.003
ELB improved by 1.09327
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.123
ELB improved by 0.879598
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.557
ELB improved by 0.566399
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.202
ELB improved by 0.355092
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.974
ELB improved by 0.227547
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.824
ELB improved by 0.150338
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.72
ELB improved by 0.103302
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.646
ELB improved by 0.0742126
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.59
ELB improved by 0.0556928
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.547
ELB improved by 0.0434384
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.512
ELB improved by 0.0349863
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.483
ELB improved by 0.0289218
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.459
ELB improved by 0.024414
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.438
ELB improved by 0.0209584
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.42
ELB improved by 0.018238
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.403
ELB improved by 0.0160471
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.389
ELB improved by 0.0142482
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.376
ELB improved by 0.012747
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.365
ELB improved by 0.0114776
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.355
ELB improved by 0.0103923
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.345
ELB improved by 0.00945618
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.185 0.187 2.362
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.051 | 0.003 | 0.053 | |
| getPIPs | 0.050 | 0.003 | 0.054 | |
| graper | 0.079 | 0.007 | 0.086 | |
| makeExampleData | 0.010 | 0.001 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.000 | 0.013 | |
| plotELBO | 0.325 | 0.024 | 0.351 | |
| plotGroupPenalties | 1.109 | 0.053 | 1.162 | |
| plotPosterior | 0.633 | 0.010 | 0.644 | |
| predict.graper | 2.071 | 0.017 | 2.089 | |
| print.graper | 0.047 | 0.003 | 0.051 | |