Britta Velten
| Snapshot Date: 2025-11-20 15:01 -0500 (Thu, 20 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_22 |
| git_last_commit: 76fc31b |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-24 12:06 -0500 (Mon, 24 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4873 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4654 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4600 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 922/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.26.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2025-11-22 06:11:47 -0500 (Sat, 22 Nov 2025) |
| EndedAt: 2025-11-22 06:13:32 -0500 (Sat, 22 Nov 2025) |
| EllapsedTime: 105.0 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.1.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 ‘1.26.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.1.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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
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=-901.79
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.46
ELB improved by 337.329
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-507.552
ELB improved by 56.9081
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.428
ELB improved by 30.1238
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.475
ELB improved by 10.9535
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.941
ELB improved by 4.53356
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.777
ELB improved by 3.16447
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.982
ELB improved by 2.79465
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.234
ELB improved by 2.74802
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.37
ELB improved by 2.8642
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.295
ELB improved by 3.07499
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.947
ELB improved by 3.34844
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.285
ELB improved by 3.66171
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.307
ELB improved by 3.97763
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.089
ELB improved by 4.21802
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.829
ELB improved by 4.25983
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.824
ELB improved by 4.00523
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.406
ELB improved by 3.41864
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.805
ELB improved by 2.6003
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.975
ELB improved by 1.83033
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.7
ELB improved by 1.27461
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.778
ELB improved by 0.922725
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.076
ELB improved by 0.701969
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.523
ELB improved by 0.553026
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.076
ELB improved by 0.446415
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.706
ELB improved by 0.369793
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.391
ELB improved by 0.315178
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.115
ELB improved by 0.275807
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.869
ELB improved by 0.246632
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.644
ELB improved by 0.22432
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.438
ELB improved by 0.206746
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.245
ELB improved by 0.192524
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.064
ELB improved by 0.180714
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.894
ELB improved by 0.170644
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.732
ELB improved by 0.161822
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.578
ELB improved by 0.153879
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.432
ELB improved by 0.146542
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.292
ELB improved by 0.139609
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.159
ELB improved by 0.132936
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.033
ELB improved by 0.126424
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.913
ELB improved by 0.120015
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.799
ELB improved by 0.113675
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.692
ELB improved by 0.107396
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.59
ELB improved by 0.101186
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.495
ELB improved by 0.0950622
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.406
ELB improved by 0.089051
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.323
ELB improved by 0.083182
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.246
ELB improved by 0.0774856
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.174
ELB improved by 0.0719911
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.107
ELB improved by 0.0667246
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.045
ELB improved by 0.0617081
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.988
ELB improved by 0.0569586
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.936
ELB improved by 0.0524878
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.887
ELB improved by 0.0483022
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.843
ELB improved by 0.0444034
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.802
ELB improved by 0.0407884
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.765
ELB improved by 0.0374509
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.73
ELB improved by 0.034381
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.699
ELB improved by 0.0315669
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.67
ELB improved by 0.0289947
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.643
ELB improved by 0.0266495
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.619
ELB improved by 0.024516
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.596
ELB improved by 0.0225784
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.575
ELB improved by 0.0208213
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.556
ELB improved by 0.0192296
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.538
ELB improved by 0.0177888
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.522
ELB improved by 0.0164854
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.506
ELB improved by 0.0153065
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.492
ELB improved by 0.0142404
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.479
ELB improved by 0.013276
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.467
ELB improved by 0.0124032
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.455
ELB improved by 0.0116131
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.444
ELB improved by 0.0108971
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.434
ELB improved by 0.0102478
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.424
ELB improved by 0.00965838
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-867.025
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-562.747
ELB improved by 304.278
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-499.522
ELB improved by 63.225
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.999
ELB improved by 33.5227
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.439
ELB improved by 12.5599
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.143
ELB improved by 5.29583
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.638
ELB improved by 3.50556
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.544
ELB improved by 3.09427
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.442
ELB improved by 3.10158
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.112
ELB improved by 3.33033
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.395
ELB improved by 3.71676
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.259
ELB improved by 4.13606
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.948
ELB improved by 4.31094
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.988
ELB improved by 3.96025
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.862
ELB improved by 3.12515
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.688
ELB improved by 2.17435
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.257
ELB improved by 1.43141
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.28
ELB improved by 0.977172
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.541
ELB improved by 0.73867
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.915
ELB improved by 0.626091
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.329
ELB improved by 0.585305
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.74
ELB improved by 0.589738
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.122
ELB improved by 0.617973
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.481
ELB improved by 0.641099
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.839
ELB improved by 0.641223
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.213
ELB improved by 0.626793
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.601
ELB improved by 0.611311
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.001
ELB improved by 0.60073
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.406
ELB improved by 0.594345
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.822
ELB improved by 0.58391
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.267
ELB improved by 0.555082
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.766
ELB improved by 0.501355
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.332
ELB improved by 0.434202
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.964
ELB improved by 0.367993
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.655
ELB improved by 0.309112
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.396
ELB improved by 0.258955
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.178
ELB improved by 0.217207
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.995
ELB improved by 0.18294
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.84
ELB improved by 0.155008
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.708
ELB improved by 0.132264
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.595
ELB improved by 0.113685
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.496
ELB improved by 0.0984129
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.41
ELB improved by 0.0857579
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.335
ELB improved by 0.075179
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.269
ELB improved by 0.066258
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.21
ELB improved by 0.0586726
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.158
ELB improved by 0.0521745
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.111
ELB improved by 0.0465708
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.07
ELB improved by 0.0417107
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.032
ELB improved by 0.0374743
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.999
ELB improved by 0.0337657
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.968
ELB improved by 0.0305069
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.94
ELB improved by 0.027634
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.915
ELB improved by 0.0250939
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.892
ELB improved by 0.0228421
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.872
ELB improved by 0.0208411
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.853
ELB improved by 0.0190591
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.835
ELB improved by 0.0174689
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.819
ELB improved by 0.0160472
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.804
ELB improved by 0.0147736
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.791
ELB improved by 0.0136309
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.778
ELB improved by 0.0126039
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.766
ELB improved by 0.0116792
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.756
ELB improved by 0.0108454
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.745
ELB improved by 0.0100925
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.736
ELB improved by 0.00941139
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-837.591
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.578
ELB improved by 271.013
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.143
ELB improved by 61.4352
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.126
ELB improved by 39.0169
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.357
ELB improved by 16.7689
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.538
ELB improved by 6.81913
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.761
ELB improved by 3.77709
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.047
ELB improved by 2.71434
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.767
ELB improved by 2.28012
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.682
ELB improved by 2.0846
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.7
ELB improved by 1.98248
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.78
ELB improved by 1.92004
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.909
ELB improved by 1.87014
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.104
ELB improved by 1.80571
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.408
ELB improved by 1.69614
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.886
ELB improved by 1.52108
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.596
ELB improved by 1.29004
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.554
ELB improved by 1.04261
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.731
ELB improved by 0.822451
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.077
ELB improved by 0.654173
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.536
ELB improved by 0.541565
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.059
ELB improved by 0.476259
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.613
ELB improved by 0.446234
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.172
ELB improved by 0.441639
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.715
ELB improved by 0.456996
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.224
ELB improved by 0.49007
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.685
ELB improved by 0.539203
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.084
ELB improved by 0.601244
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.413
ELB improved by 0.671057
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.67
ELB improved by 0.742782
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.858
ELB improved by 0.812472
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.978
ELB improved by 0.879888
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.033
ELB improved by 0.945207
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.031
ELB improved by 1.00127
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.994
ELB improved by 1.03765
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.933
ELB improved by 1.06023
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.841
ELB improved by 1.09259
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.688
ELB improved by 1.153
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.491
ELB improved by 1.19699
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.375
ELB improved by 1.11575
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.444
ELB improved by 0.93154
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.708
ELB improved by 0.735648
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.147
ELB improved by 0.560758
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.731
ELB improved by 0.416035
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.427
ELB improved by 0.303725
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.207
ELB improved by 0.220739
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.045
ELB improved by 0.161237
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.926
ELB improved by 0.11916
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.837
ELB improved by 0.0894813
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.768
ELB improved by 0.0684442
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.715
ELB improved by 0.0533868
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.672
ELB improved by 0.0424716
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.638
ELB improved by 0.0344451
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.61
ELB improved by 0.0284535
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.586
ELB improved by 0.0239122
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.565
ELB improved by 0.0204172
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.548
ELB improved by 0.0176864
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.532
ELB improved by 0.0155203
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.518
ELB improved by 0.0137765
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.506
ELB improved by 0.0123524
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.495
ELB improved by 0.011173
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.485
ELB improved by 0.0101832
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.475
ELB improved by 0.00934207
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-878.058
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-548.483
ELB improved by 329.575
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-493.788
ELB improved by 54.6957
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.732
ELB improved by 27.056
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.866
ELB improved by 11.8659
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.257
ELB improved by 6.6091
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.026
ELB improved by 5.23049
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.783
ELB improved by 5.24334
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.075
ELB improved by 5.70816
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.069
ELB improved by 6.00542
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.517
ELB improved by 5.55216
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.214
ELB improved by 4.3031
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.325
ELB improved by 2.88895
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.481
ELB improved by 1.84365
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.253
ELB improved by 1.22812
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.339
ELB improved by 0.913839
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.537
ELB improved by 0.802033
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.695
ELB improved by 0.842402
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.814
ELB improved by 0.880733
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.1
ELB improved by 0.714471
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.584
ELB improved by 0.516132
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.164
ELB improved by 0.419714
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.781
ELB improved by 0.382865
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.427
ELB improved by 0.35434
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.12
ELB improved by 0.306455
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.874
ELB improved by 0.246363
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.68
ELB improved by 0.193973
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.524
ELB improved by 0.156121
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.394
ELB improved by 0.130112
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.282
ELB improved by 0.111926
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.183
ELB improved by 0.098648
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.095
ELB improved by 0.0884876
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.014
ELB improved by 0.0804015
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.94
ELB improved by 0.0737799
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.872
ELB improved by 0.0682504
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.809
ELB improved by 0.0635715
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.749
ELB improved by 0.0595761
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.693
ELB improved by 0.056142
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.64
ELB improved by 0.0531765
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.589
ELB improved by 0.0506058
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.541
ELB improved by 0.0483704
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.494
ELB improved by 0.04642
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.45
ELB improved by 0.044712
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.406
ELB improved by 0.0432088
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.365
ELB improved by 0.0418775
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.324
ELB improved by 0.0406885
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.284
ELB improved by 0.039616
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.246
ELB improved by 0.038638
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.208
ELB improved by 0.0377364
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.171
ELB improved by 0.0368976
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.135
ELB improved by 0.0361125
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.099
ELB improved by 0.0353764
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.065
ELB improved by 0.034688
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.031
ELB improved by 0.0340493
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.997
ELB improved by 0.0334641
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.964
ELB improved by 0.0329373
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.932
ELB improved by 0.0324745
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.9
ELB improved by 0.0320814
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.868
ELB improved by 0.0317636
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.836
ELB improved by 0.0315273
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.805
ELB improved by 0.0313787
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.774
ELB improved by 0.031325
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.742
ELB improved by 0.0313747
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.711
ELB improved by 0.0315381
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.679
ELB improved by 0.0318279
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.647
ELB improved by 0.0322605
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.614
ELB improved by 0.0328572
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.58
ELB improved by 0.0336464
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.546
ELB improved by 0.0346679
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.51
ELB improved by 0.0359785
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.472
ELB improved by 0.037663
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.432
ELB improved by 0.0398523
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.389
ELB improved by 0.0427541
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.343
ELB improved by 0.0467042
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.29
ELB improved by 0.0522512
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.23
ELB improved by 0.0602836
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.158
ELB improved by 0.0721732
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.068
ELB improved by 0.0897506
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.954
ELB improved by 0.114481
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.809
ELB improved by 0.144765
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.636
ELB improved by 0.17254
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.449
ELB improved by 0.187005
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.263
ELB improved by 0.18659
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.084
ELB improved by 0.178809
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.915
ELB improved by 0.169118
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.756
ELB improved by 0.158992
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.607
ELB improved by 0.149059
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.467
ELB improved by 0.140289
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.332
ELB improved by 0.134128
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.2
ELB improved by 0.132609
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.062
ELB improved by 0.138251
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.909
ELB improved by 0.152417
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.739
ELB improved by 0.170358
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.561
ELB improved by 0.177723
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.398
ELB improved by 0.163073
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.265
ELB improved by 0.133479
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.161
ELB improved by 0.103061
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.083
ELB improved by 0.0784023
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.023
ELB improved by 0.059839
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.977
ELB improved by 0.0459708
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.942
ELB improved by 0.0354903
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.914
ELB improved by 0.027486
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.893
ELB improved by 0.0213469
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.876
ELB improved by 0.0166427
iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.863
ELB improved by 0.0130507
iteration 106
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.853
ELB improved by 0.0103185
iteration 107
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.845
ELB improved by 0.00824623
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
3.189 0.265 4.654
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.035 | 0.019 | 0.056 | |
| getPIPs | 0.030 | 0.013 | 0.060 | |
| graper | 0.050 | 0.023 | 0.076 | |
| makeExampleData | 0.006 | 0.002 | 0.009 | |
| makeExampleDataWithUnequalGroups | 0.027 | 0.003 | 0.045 | |
| plotELBO | 0.351 | 0.018 | 0.486 | |
| plotGroupPenalties | 1.405 | 0.050 | 1.966 | |
| plotPosterior | 0.682 | 0.020 | 0.919 | |
| predict.graper | 0.538 | 0.117 | 0.957 | |
| print.graper | 0.032 | 0.013 | 0.070 | |