Britta Velten
| Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 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 2025-08-30 12:07 -0400 (Sat, 30 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 907/2320 | 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.25.2.tar.gz |
| StartedAt: 2025-08-29 19:44:38 -0400 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 19:45:04 -0400 (Fri, 29 Aug 2025) |
| EllapsedTime: 26.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.25.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.25.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.25.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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=-862.429
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-593.758
ELB improved by 268.671
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-536.099
ELB improved by 57.6591
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.196
ELB improved by 44.9025
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.796
ELB improved by 22.4001
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.809
ELB improved by 9.98746
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.631
ELB improved by 6.17738
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.146
ELB improved by 5.48522
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.273
ELB improved by 5.87349
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.815
ELB improved by 6.45737
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.276
ELB improved by 6.5397
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.567
ELB improved by 5.70855
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.335
ELB improved by 4.23195
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.557
ELB improved by 2.77845
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.818
ELB improved by 1.73916
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.707
ELB improved by 1.11014
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.955
ELB improved by 0.752407
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.408
ELB improved by 0.547091
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.985
ELB improved by 0.422832
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.643
ELB improved by 0.342255
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.356
ELB improved by 0.286619
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.11
ELB improved by 0.246436
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.893
ELB improved by 0.216736
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.698
ELB improved by 0.194825
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.519
ELB improved by 0.179193
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.35
ELB improved by 0.16891
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.187
ELB improved by 0.163148
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.026
ELB improved by 0.160731
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.866
ELB improved by 0.159831
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.709
ELB improved by 0.157931
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.557
ELB improved by 0.151886
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.418
ELB improved by 0.138507
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.301
ELB improved by 0.117237
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.208
ELB improved by 0.0928034
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.136
ELB improved by 0.0719674
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.078
ELB improved by 0.0577822
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.029
ELB improved by 0.0492087
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.985
ELB improved by 0.0440708
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.944
ELB improved by 0.0407695
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.906
ELB improved by 0.0384471
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.869
ELB improved by 0.0367008
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.834
ELB improved by 0.0353478
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.799
ELB improved by 0.0343025
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.766
ELB improved by 0.0335208
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.733
ELB improved by 0.0329773
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.7
ELB improved by 0.0326564
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.668
ELB improved by 0.0325485
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.635
ELB improved by 0.032648
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.602
ELB improved by 0.032953
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.569
ELB improved by 0.0334648
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.535
ELB improved by 0.0341879
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.499
ELB improved by 0.0351301
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.463
ELB improved by 0.0363022
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.425
ELB improved by 0.0377189
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.386
ELB improved by 0.0393986
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.345
ELB improved by 0.0413641
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.301
ELB improved by 0.0436431
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.255
ELB improved by 0.0462693
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.205
ELB improved by 0.0492828
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.153
ELB improved by 0.0527321
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.096
ELB improved by 0.0566752
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.035
ELB improved by 0.0611823
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.968
ELB improved by 0.0663389
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.896
ELB improved by 0.0722495
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.817
ELB improved by 0.0790436
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.73
ELB improved by 0.0868837
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.634
ELB improved by 0.0959758
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.528
ELB improved by 0.106586
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.409
ELB improved by 0.11906
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.275
ELB improved by 0.133859
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.123
ELB improved by 0.151597
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.95
ELB improved by 0.173095
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.751
ELB improved by 0.199433
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.519
ELB improved by 0.231941
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.247
ELB improved by 0.271989
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.926
ELB improved by 0.320277
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.551
ELB improved by 0.37545
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.118
ELB improved by 0.433092
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.63
ELB improved by 0.487718
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.093
ELB improved by 0.536888
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.515
ELB improved by 0.578693
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.914
ELB improved by 0.601006
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.328
ELB improved by 0.58534
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.795
ELB improved by 0.532837
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.333
ELB improved by 0.462863
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.943
ELB improved by 0.389833
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.622
ELB improved by 0.321237
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.36
ELB improved by 0.261486
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.149
ELB improved by 0.211458
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.979
ELB improved by 0.169669
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.844
ELB improved by 0.134713
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.738
ELB improved by 0.106091
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.655
ELB improved by 0.0835207
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.588
ELB improved by 0.0663054
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.535
ELB improved by 0.0534122
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.491
ELB improved by 0.0437976
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.454
ELB improved by 0.0366062
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.423
ELB improved by 0.0312045
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.396
ELB improved by 0.0271441
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.372
ELB improved by 0.0241161
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.35
ELB improved by 0.0219161
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.33
ELB improved by 0.0204202
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.31
ELB improved by 0.0195652
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.291
ELB improved by 0.0193318
iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.271
ELB improved by 0.0197208
iteration 106
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.25
ELB improved by 0.020714
iteration 107
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.228
ELB improved by 0.0222025
iteration 108
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.204
ELB improved by 0.023881
iteration 109
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.179
ELB improved by 0.0251648
iteration 110
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.154
ELB improved by 0.025275
iteration 111
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.13
ELB improved by 0.0236174
iteration 112
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.11
ELB improved by 0.0202588
iteration 113
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.094
ELB improved by 0.0159918
iteration 114
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.082
ELB improved by 0.0118336
iteration 115
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.074
ELB improved by 0.00846252
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-810.114
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-563.684
ELB improved by 246.43
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-503.578
ELB improved by 60.1059
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.959
ELB improved by 43.6196
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.363
ELB improved by 23.5957
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.441
ELB improved by 10.922
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.882
ELB improved by 6.55911
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.019
ELB improved by 5.86289
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.631
ELB improved by 6.38806
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.118
ELB improved by 7.51345
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.531
ELB improved by 8.58652
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.026
ELB improved by 8.50485
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.243
ELB improved by 6.78285
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.81
ELB improved by 4.43321
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.216
ELB improved by 2.59387
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.704
ELB improved by 1.51213
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.764
ELB improved by 0.940005
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.126
ELB improved by 0.638469
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-364.653
ELB improved by 0.472375
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-364.279
ELB improved by 0.374696
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-363.965
ELB improved by 0.313063
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-363.694
ELB improved by 0.271496
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-363.452
ELB improved by 0.2417
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-363.233
ELB improved by 0.219095
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-363.032
ELB improved by 0.201011
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-362.846
ELB improved by 0.185825
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-362.674
ELB improved by 0.172523
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-362.513
ELB improved by 0.160475
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-362.364
ELB improved by 0.149293
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-362.225
ELB improved by 0.138751
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-362.097
ELB improved by 0.128728
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.977
ELB improved by 0.119175
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.867
ELB improved by 0.11008
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.766
ELB improved by 0.101455
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.673
ELB improved by 0.093318
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.587
ELB improved by 0.085686
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.508
ELB improved by 0.0785696
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.436
ELB improved by 0.0719704
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.37
ELB improved by 0.065881
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.31
ELB improved by 0.0602859
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.255
ELB improved by 0.0551628
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.205
ELB improved by 0.0504851
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.158
ELB improved by 0.0462231
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.116
ELB improved by 0.0423456
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.077
ELB improved by 0.0388214
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.041
ELB improved by 0.03562
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.009
ELB improved by 0.0327123
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.979
ELB improved by 0.030071
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.951
ELB improved by 0.0276707
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.926
ELB improved by 0.0254881
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.902
ELB improved by 0.0235021
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.88
ELB improved by 0.0216936
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.86
ELB improved by 0.0200451
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.842
ELB improved by 0.0185411
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.825
ELB improved by 0.0171677
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.809
ELB improved by 0.0159123
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.794
ELB improved by 0.0147637
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.78
ELB improved by 0.0137117
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.767
ELB improved by 0.0127475
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.756
ELB improved by 0.0118627
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.745
ELB improved by 0.0110502
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.734
ELB improved by 0.0103034
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.725
ELB improved by 0.00961646
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-865.678
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.928
ELB improved by 291.75
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.245
ELB improved by 62.6834
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.317
ELB improved by 38.9279
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.648
ELB improved by 15.6687
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.711
ELB improved by 5.93679
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.698
ELB improved by 3.01371
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.527
ELB improved by 2.17088
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.565
ELB improved by 1.96179
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.573
ELB improved by 1.99182
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.408
ELB improved by 2.16541
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.946
ELB improved by 2.46154
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.079
ELB improved by 2.86702
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.76
ELB improved by 3.31916
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.112
ELB improved by 3.64777
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.511
ELB improved by 3.60142
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.437
ELB improved by 3.07348
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.14
ELB improved by 2.29705
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.535
ELB improved by 1.60492
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.413
ELB improved by 1.12256
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.594
ELB improved by 0.818874
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.953
ELB improved by 0.641197
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.407
ELB improved by 0.545179
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.91
ELB improved by 0.497602
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.432
ELB improved by 0.478104
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.956
ELB improved by 0.475776
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.471
ELB improved by 0.485308
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.965
ELB improved by 0.505306
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.427
ELB improved by 0.538668
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.831
ELB improved by 0.59542
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.132
ELB improved by 0.698937
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.246
ELB improved by 0.886752
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.079
ELB improved by 1.16633
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.569
ELB improved by 1.51034
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.577
ELB improved by 1.99235
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.138
ELB improved by 2.43834
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.537
ELB improved by 2.60097
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.947
ELB improved by 2.59021
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.496
ELB improved by 2.45075
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.123
ELB improved by 2.37323
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.777
ELB improved by 2.34631
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.769
ELB improved by 2.00792
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.015
ELB improved by 1.75416
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.704
ELB improved by 1.31032
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.947
ELB improved by 0.757072
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.519
ELB improved by 0.428641
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.25
ELB improved by 0.26868
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.062
ELB improved by 0.187613
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.921
ELB improved by 0.141687
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.808
ELB improved by 0.112352
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.717
ELB improved by 0.0916741
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.641
ELB improved by 0.0760532
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.577
ELB improved by 0.0637392
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.523
ELB improved by 0.0538143
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.477
ELB improved by 0.0457392
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.438
ELB improved by 0.0391463
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.404
ELB improved by 0.0337498
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.375
ELB improved by 0.0293154
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.349
ELB improved by 0.0256497
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.327
ELB improved by 0.0225972
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.307
ELB improved by 0.0200353
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.289
ELB improved by 0.0178687
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.273
ELB improved by 0.0160238
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.258
ELB improved by 0.0144434
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.245
ELB improved by 0.0130825
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.233
ELB improved by 0.0119056
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.223
ELB improved by 0.0108837
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.213
ELB improved by 0.00999339
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-859.848
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-556.993
ELB improved by 302.855
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-502.59
ELB improved by 54.4024
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.604
ELB improved by 28.9867
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.019
ELB improved by 12.5844
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.452
ELB improved by 5.56731
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.961
ELB improved by 3.49116
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.102
ELB improved by 2.85925
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.489
ELB improved by 2.61252
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.988
ELB improved by 2.50136
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.533
ELB improved by 2.45472
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.079
ELB improved by 2.45349
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.584
ELB improved by 2.49581
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.006
ELB improved by 2.57793
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.328
ELB improved by 2.67732
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.59
ELB improved by 2.73803
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.912
ELB improved by 2.67859
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.48
ELB improved by 2.43132
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.476
ELB improved by 2.00456
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.971
ELB improved by 1.505
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.917
ELB improved by 1.05408
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.206
ELB improved by 0.711127
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.727
ELB improved by 0.479034
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.392
ELB improved by 0.334222
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.145
ELB improved by 0.247068
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.952
ELB improved by 0.193695
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.793
ELB improved by 0.159056
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.658
ELB improved by 0.134851
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.541
ELB improved by 0.116732
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.439
ELB improved by 0.102423
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.348
ELB improved by 0.0906896
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.267
ELB improved by 0.0808222
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.195
ELB improved by 0.0723837
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.13
ELB improved by 0.065084
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.071
ELB improved by 0.0587176
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.018
ELB improved by 0.053131
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.97
ELB improved by 0.0482051
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.926
ELB improved by 0.0438446
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.886
ELB improved by 0.0399713
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.849
ELB improved by 0.0365205
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.816
ELB improved by 0.0334377
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.785
ELB improved by 0.0306765
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.757
ELB improved by 0.0281975
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.731
ELB improved by 0.0259666
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.707
ELB improved by 0.0239547
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.685
ELB improved by 0.0221364
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.664
ELB improved by 0.0204898
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.645
ELB improved by 0.0189959
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.628
ELB improved by 0.0176379
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.611
ELB improved by 0.0164014
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.596
ELB improved by 0.0152737
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.582
ELB improved by 0.0142435
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.568
ELB improved by 0.013301
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.556
ELB improved by 0.0124376
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.544
ELB improved by 0.0116455
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.533
ELB improved by 0.0109178
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.523
ELB improved by 0.0102486
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.514
ELB improved by 0.00963245
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
0.894 0.078 1.003
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.028 | 0.008 | 0.036 | |
| getPIPs | 0.027 | 0.006 | 0.033 | |
| graper | 0.043 | 0.010 | 0.053 | |
| makeExampleData | 0.003 | 0.000 | 0.005 | |
| makeExampleDataWithUnequalGroups | 0.004 | 0.001 | 0.005 | |
| plotELBO | 0.102 | 0.009 | 0.111 | |
| plotGroupPenalties | 0.230 | 0.007 | 0.240 | |
| plotPosterior | 0.170 | 0.005 | 0.175 | |
| predict.graper | 1.023 | 0.035 | 1.061 | |
| print.graper | 0.027 | 0.004 | 0.035 | |