Britta Velten
| Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 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 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| 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 905/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.25.2 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.25.2 |
| 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: 2025-08-08 21:27:20 -0400 (Fri, 08 Aug 2025) |
| EndedAt: 2025-08-08 21:28:32 -0400 (Fri, 08 Aug 2025) |
| EllapsedTime: 72.1 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 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 14.0.0 (clang-1400.0.29.202)’
* 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-x86_64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.25.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/x86_64-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-x86_64/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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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=-896.785
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-597.929
ELB improved by 298.856
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-534.569
ELB improved by 63.3605
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.707
ELB improved by 43.862
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.098
ELB improved by 20.6086
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.342
ELB improved by 8.75636
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.337
ELB improved by 5.00409
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.561
ELB improved by 3.77657
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.265
ELB improved by 3.29602
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.231
ELB improved by 3.03369
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.421
ELB improved by 2.81005
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.873
ELB improved by 2.54836
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.657
ELB improved by 2.21585
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.835
ELB improved by 1.82187
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.42
ELB improved by 1.4152
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.364
ELB improved by 1.05587
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.583
ELB improved by 0.780802
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.991
ELB improved by 0.592315
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.52
ELB improved by 0.4704
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.129
ELB improved by 0.391015
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.793
ELB improved by 0.336711
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.495
ELB improved by 0.297881
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.225
ELB improved by 0.26965
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.976
ELB improved by 0.249114
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.742
ELB improved by 0.23421
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.518
ELB improved by 0.223448
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.303
ELB improved by 0.215792
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.092
ELB improved by 0.21054
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.885
ELB improved by 0.207221
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.679
ELB improved by 0.205522
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.474
ELB improved by 0.205245
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.268
ELB improved by 0.206285
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.059
ELB improved by 0.208612
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.847
ELB improved by 0.21226
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.63
ELB improved by 0.217322
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.406
ELB improved by 0.223939
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.173
ELB improved by 0.232284
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.931
ELB improved by 0.24256
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.676
ELB improved by 0.254986
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.406
ELB improved by 0.26979
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.119
ELB improved by 0.287224
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.811
ELB improved by 0.3076
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.48
ELB improved by 0.331368
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.121
ELB improved by 0.359126
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.73
ELB improved by 0.391152
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.304
ELB improved by 0.425402
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.85
ELB improved by 0.453933
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.387
ELB improved by 0.463665
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.939
ELB improved by 0.447861
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.525
ELB improved by 0.413378
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.154
ELB improved by 0.371272
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.826
ELB improved by 0.328359
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.538
ELB improved by 0.287637
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.288
ELB improved by 0.250465
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.07
ELB improved by 0.217453
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.882
ELB improved by 0.188677
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.718
ELB improved by 0.163826
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.575
ELB improved by 0.142395
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.451
ELB improved by 0.12388
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.344
ELB improved by 0.107885
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.249
ELB improved by 0.094145
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.167
ELB improved by 0.0824907
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.094
ELB improved by 0.0727923
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.029
ELB improved by 0.0649061
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.971
ELB improved by 0.0586323
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.917
ELB improved by 0.0536714
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.867
ELB improved by 0.0495833
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.822
ELB improved by 0.0457934
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.78
ELB improved by 0.0417223
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.743
ELB improved by 0.0370432
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.711
ELB improved by 0.0318893
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.684
ELB improved by 0.026765
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.662
ELB improved by 0.0221988
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.643
ELB improved by 0.0184597
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.628
ELB improved by 0.0155363
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.615
ELB improved by 0.0132743
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.603
ELB improved by 0.0115018
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.593
ELB improved by 0.0100826
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.584
ELB improved by 0.00892294
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-879.866
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-583.634
ELB improved by 296.232
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-522.348
ELB improved by 61.2858
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.758
ELB improved by 42.59
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.6
ELB improved by 19.1573
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.654
ELB improved by 7.94659
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.195
ELB improved by 4.45846
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.698
ELB improved by 3.49699
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.43
ELB improved by 3.268
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.121
ELB improved by 3.30973
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.647
ELB improved by 3.47412
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.941
ELB improved by 3.706
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.983
ELB improved by 3.95771
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.861
ELB improved by 4.12191
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.868
ELB improved by 3.9931
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.437
ELB improved by 3.43048
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.826
ELB improved by 2.61138
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.979
ELB improved by 1.84703
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.704
ELB improved by 1.27485
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.822
ELB improved by 0.882009
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.183
ELB improved by 0.639633
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.674
ELB improved by 0.508795
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.229
ELB improved by 0.444692
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.812
ELB improved by 0.417469
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.399
ELB improved by 0.412209
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.978
ELB improved by 0.421204
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.54
ELB improved by 0.43854
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.081
ELB improved by 0.458776
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.602
ELB improved by 0.479195
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.101
ELB improved by 0.500984
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.574
ELB improved by 0.526252
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.019
ELB improved by 0.555339
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.432
ELB improved by 0.587112
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.812
ELB improved by 0.619957
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.16
ELB improved by 0.652031
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.479
ELB improved by 0.681058
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.775
ELB improved by 0.70415
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.057
ELB improved by 0.717832
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.339
ELB improved by 0.71828
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.637
ELB improved by 0.701683
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.972
ELB improved by 0.664963
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.365
ELB improved by 0.607449
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.831
ELB improved by 0.533161
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.38
ELB improved by 0.451012
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.009
ELB improved by 0.371196
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.708
ELB improved by 0.300849
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.466
ELB improved by 0.242697
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.269
ELB improved by 0.196426
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.109
ELB improved by 0.160557
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.975
ELB improved by 0.133622
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.86
ELB improved by 0.114653
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.757
ELB improved by 0.103366
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.657
ELB improved by 0.100137
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.551
ELB improved by 0.105372
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.434
ELB improved by 0.117254
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.306
ELB improved by 0.128452
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.177
ELB improved by 0.128635
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.061
ELB improved by 0.116082
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.962
ELB improved by 0.0994288
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.876
ELB improved by 0.0852906
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.802
ELB improved by 0.0743535
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.737
ELB improved by 0.0653482
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.679
ELB improved by 0.0573647
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.629
ELB improved by 0.050122
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.585
ELB improved by 0.0436709
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.547
ELB improved by 0.0381013
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.514
ELB improved by 0.0334057
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.484
ELB improved by 0.0294832
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.458
ELB improved by 0.0261956
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.435
ELB improved by 0.0234124
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.414
ELB improved by 0.021029
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.395
ELB improved by 0.0189673
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.378
ELB improved by 0.0171697
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.362
ELB improved by 0.0155929
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.348
ELB improved by 0.0142036
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.335
ELB improved by 0.0129749
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.323
ELB improved by 0.0118851
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.312
ELB improved by 0.0109158
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.302
ELB improved by 0.0100517
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.293
ELB improved by 0.00927973
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-923.42
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-572.193
ELB improved by 351.227
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.382
ELB improved by 57.811
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.471
ELB improved by 28.9108
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.032
ELB improved by 11.4395
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.636
ELB improved by 5.39529
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.493
ELB improved by 4.14359
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.406
ELB improved by 4.08669
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.956
ELB improved by 4.45054
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.896
ELB improved by 5.05955
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.153
ELB improved by 5.74328
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.111
ELB improved by 6.04152
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.762
ELB improved by 5.34946
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.834
ELB improved by 3.92796
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.143
ELB improved by 2.6904
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.139
ELB improved by 2.0046
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.374
ELB improved by 1.76472
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.604
ELB improved by 1.77021
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.761
ELB improved by 1.84307
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.809
ELB improved by 1.95227
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.633
ELB improved by 2.17596
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.095
ELB improved by 2.5371
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.27
ELB improved by 2.82531
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.294
ELB improved by 2.97646
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.256
ELB improved by 3.03788
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.379
ELB improved by 2.87669
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.964
ELB improved by 2.41484
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.194
ELB improved by 1.77039
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.027
ELB improved by 1.16684
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.291
ELB improved by 0.735703
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.82
ELB improved by 0.471494
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.503
ELB improved by 0.317056
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.278
ELB improved by 0.224751
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.111
ELB improved by 0.16667
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.983
ELB improved by 0.128063
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.882
ELB improved by 0.101159
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.8
ELB improved by 0.081689
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.733
ELB improved by 0.0671651
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.677
ELB improved by 0.0560575
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.63
ELB improved by 0.0473823
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.589
ELB improved by 0.0404854
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.554
ELB improved by 0.0349193
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.524
ELB improved by 0.03037
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.497
ELB improved by 0.0266117
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.474
ELB improved by 0.0234782
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.453
ELB improved by 0.0208449
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.435
ELB improved by 0.0186163
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.418
ELB improved by 0.0167186
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.403
ELB improved by 0.0150937
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.389
ELB improved by 0.0136953
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.377
ELB improved by 0.0124863
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.365
ELB improved by 0.0114365
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.355
ELB improved by 0.0105213
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.345
ELB improved by 0.00972043
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-864.523
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.079
ELB improved by 293.443
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-509.269
ELB improved by 61.8103
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.681
ELB improved by 41.5878
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.833
ELB improved by 18.8481
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.06
ELB improved by 7.7731
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.995
ELB improved by 4.06518
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.129
ELB improved by 2.86533
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.665
ELB improved by 2.46434
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.312
ELB improved by 2.35264
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.939
ELB improved by 2.37338
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.486
ELB improved by 2.45313
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.955
ELB improved by 2.53078
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.417
ELB improved by 2.53799
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.001
ELB improved by 2.41588
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.862
ELB improved by 2.13945
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.115
ELB improved by 1.74718
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.751
ELB improved by 1.36393
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.655
ELB improved by 1.09572
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.708
ELB improved by 0.946878
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.838
ELB improved by 0.86959
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.018
ELB improved by 0.820059
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.244
ELB improved by 0.774016
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.523
ELB improved by 0.721827
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.86
ELB improved by 0.662316
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.261
ELB improved by 0.598758
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.726
ELB improved by 0.535735
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.249
ELB improved by 0.477045
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.824
ELB improved by 0.424923
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.444
ELB improved by 0.380182
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.101
ELB improved by 0.342669
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.789
ELB improved by 0.311699
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.503
ELB improved by 0.286361
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.237
ELB improved by 0.265709
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.988
ELB improved by 0.248889
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.753
ELB improved by 0.235222
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.529
ELB improved by 0.224288
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.313
ELB improved by 0.216034
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.102
ELB improved by 0.210962
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.891
ELB improved by 0.210482
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.674
ELB improved by 0.217522
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.437
ELB improved by 0.237081
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.163
ELB improved by 0.274083
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.841
ELB improved by 0.321305
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.496
ELB improved by 0.345673
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.172
ELB improved by 0.323344
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.894
ELB improved by 0.278003
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.658
ELB improved by 0.236339
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.455
ELB improved by 0.202717
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.282
ELB improved by 0.173685
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.135
ELB improved by 0.14686
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.013
ELB improved by 0.121968
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.913
ELB improved by 0.0998706
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.831
ELB improved by 0.0813736
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.765
ELB improved by 0.066591
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.71
ELB improved by 0.0550389
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.664
ELB improved by 0.0460227
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.625
ELB improved by 0.0389111
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.592
ELB improved by 0.0332263
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.563
ELB improved by 0.0286298
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.538
ELB improved by 0.0248835
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.516
ELB improved by 0.0218148
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.497
ELB improved by 0.0192939
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.48
ELB improved by 0.0172208
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.464
ELB improved by 0.0155165
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.45
ELB improved by 0.0141181
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.437
ELB improved by 0.0129756
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.425
ELB improved by 0.0120491
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.414
ELB improved by 0.0113066
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.403
ELB improved by 0.0107228
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.393
ELB improved by 0.0102767
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.383
ELB improved by 0.00995106
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.493 0.260 2.756
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.052 | 0.018 | 0.070 | |
| getPIPs | 0.047 | 0.013 | 0.060 | |
| graper | 0.078 | 0.020 | 0.098 | |
| makeExampleData | 0.009 | 0.001 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.001 | 0.013 | |
| plotELBO | 0.265 | 0.021 | 0.287 | |
| plotGroupPenalties | 0.816 | 0.016 | 0.837 | |
| plotPosterior | 0.588 | 0.020 | 0.616 | |
| predict.graper | 1.928 | 0.088 | 2.032 | |
| print.graper | 0.052 | 0.014 | 0.066 | |