Britta Velten
| Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 82b0592 |
| git_last_commit_date: 2025-06-24 03:15:40 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-26 12:06 -0400 (Fri, 26 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4831 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4619 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4563 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 913/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.25.2 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.25.2 |
| Command: /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: 2025-09-25 19:45:52 -0400 (Thu, 25 Sep 2025) |
| EndedAt: 2025-09-25 19:46:22 -0400 (Thu, 25 Sep 2025) |
| EllapsedTime: 29.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.25.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.25.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.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 ‘1.25.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-841.799
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.156
ELB improved by 266.643
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.003
ELB improved by 62.153
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.92
ELB improved by 45.083
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.231
ELB improved by 20.6886
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.534
ELB improved by 7.6977
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.313
ELB improved by 4.22033
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.029
ELB improved by 3.28454
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.93
ELB improved by 3.09887
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.694
ELB improved by 3.23624
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.163
ELB improved by 3.53053
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.294
ELB improved by 3.86936
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.204
ELB improved by 4.08993
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.231
ELB improved by 3.97239
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.819
ELB improved by 3.41215
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.227
ELB improved by 2.59183
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.412
ELB improved by 1.81539
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.172
ELB improved by 1.23973
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.307
ELB improved by 0.864925
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.669
ELB improved by 0.638555
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.16
ELB improved by 0.508699
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.721
ELB improved by 0.43859
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.315
ELB improved by 0.406345
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.916
ELB improved by 0.398996
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.51
ELB improved by 0.405725
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.096
ELB improved by 0.414159
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.68
ELB improved by 0.416421
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.262
ELB improved by 0.417559
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.834
ELB improved by 0.428414
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.378
ELB improved by 0.455836
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.873
ELB improved by 0.504617
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.29
ELB improved by 0.583352
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.579
ELB improved by 0.71102
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.649
ELB improved by 0.929524
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.329
ELB improved by 1.32041
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.382
ELB improved by 1.94725
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.788
ELB improved by 2.59404
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.014
ELB improved by 2.77424
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.488
ELB improved by 2.52581
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.384
ELB improved by 2.10387
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.752
ELB improved by 1.63194
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.539
ELB improved by 1.21331
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.63
ELB improved by 0.908237
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.924
ELB improved by 0.706312
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.373
ELB improved by 0.551502
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.953
ELB improved by 0.419453
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.635
ELB improved by 0.318142
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.392
ELB improved by 0.243389
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.204
ELB improved by 0.187259
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.054
ELB improved by 0.150178
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.92
ELB improved by 0.134263
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.781
ELB improved by 0.139072
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.618
ELB improved by 0.163183
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.419
ELB improved by 0.198369
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.201
ELB improved by 0.218363
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.005
ELB improved by 0.1956
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.864
ELB improved by 0.141391
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.775
ELB improved by 0.0892694
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.72
ELB improved by 0.0543532
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.686
ELB improved by 0.0344267
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.662
ELB improved by 0.0236206
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.645
ELB improved by 0.0176077
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.631
ELB improved by 0.0139731
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.619
ELB improved by 0.0115384
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.609
ELB improved by 0.00976558
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-894.502
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.235
ELB improved by 310.266
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-522.018
ELB improved by 62.2175
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.441
ELB improved by 38.5769
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.417
ELB improved by 16.0238
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.708
ELB improved by 6.70909
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.034
ELB improved by 4.67414
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.692
ELB improved by 4.34147
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.272
ELB improved by 4.42059
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.683
ELB improved by 4.589
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.046
ELB improved by 4.63714
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.654
ELB improved by 4.3919
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.866
ELB improved by 3.78746
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.933
ELB improved by 2.93365
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.853
ELB improved by 2.08005
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.433
ELB improved by 1.41977
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.45
ELB improved by 0.983413
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.74
ELB improved by 0.709527
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.21
ELB improved by 0.530352
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.805
ELB improved by 0.404538
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.492
ELB improved by 0.313467
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.244
ELB improved by 0.248112
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.042
ELB improved by 0.201537
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.874
ELB improved by 0.167827
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.732
ELB improved by 0.142631
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.608
ELB improved by 0.123111
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.501
ELB improved by 0.107509
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.406
ELB improved by 0.0947289
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.322
ELB improved by 0.0840641
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.247
ELB improved by 0.0750359
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.18
ELB improved by 0.067307
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.119
ELB improved by 0.0606299
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.064
ELB improved by 0.0548179
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.015
ELB improved by 0.0497267
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.969
ELB improved by 0.0452425
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.928
ELB improved by 0.0412742
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.89
ELB improved by 0.0377479
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.856
ELB improved by 0.034603
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.824
ELB improved by 0.0317892
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.795
ELB improved by 0.0292643
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.768
ELB improved by 0.0269928
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.743
ELB improved by 0.0249444
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.72
ELB improved by 0.0230933
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.698
ELB improved by 0.0214171
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.678
ELB improved by 0.0198964
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.66
ELB improved by 0.0185145
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.643
ELB improved by 0.0172567
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.626
ELB improved by 0.01611
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.611
ELB improved by 0.0150632
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.597
ELB improved by 0.0141062
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.584
ELB improved by 0.0132302
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.572
ELB improved by 0.0124273
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.56
ELB improved by 0.0116905
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.549
ELB improved by 0.0110137
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.539
ELB improved by 0.0103913
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.529
ELB improved by 0.00981836
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-883.725
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-574.955
ELB improved by 308.77
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.43
ELB improved by 58.5246
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.867
ELB improved by 34.5638
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.586
ELB improved by 14.2802
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.145
ELB improved by 6.44146
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.518
ELB improved by 4.62695
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.031
ELB improved by 4.48681
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.247
ELB improved by 4.78362
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.176
ELB improved by 5.0719
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.19
ELB improved by 4.98557
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.897
ELB improved by 4.29309
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.696
ELB improved by 3.20118
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.551
ELB improved by 2.14493
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.189
ELB improved by 1.36138
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.315
ELB improved by 0.8746
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.712
ELB improved by 0.602984
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.259
ELB improved by 0.452613
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.895
ELB improved by 0.364169
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.587
ELB improved by 0.308045
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.317
ELB improved by 0.2705
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.071
ELB improved by 0.245606
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.839
ELB improved by 0.232263
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.604
ELB improved by 0.234765
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.336
ELB improved by 0.268147
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.969
ELB improved by 0.366688
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.432
ELB improved by 0.536885
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.821
ELB improved by 0.610871
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.336
ELB improved by 0.485469
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.992
ELB improved by 0.343783
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.713
ELB improved by 0.279431
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.45
ELB improved by 0.262813
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.185
ELB improved by 0.264477
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.913
ELB improved by 0.272714
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.629
ELB improved by 0.283636
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.333
ELB improved by 0.295882
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.024
ELB improved by 0.308885
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.702
ELB improved by 0.322398
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.365
ELB improved by 0.336401
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.014
ELB improved by 0.351106
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.647
ELB improved by 0.366933
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.263
ELB improved by 0.384276
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.86
ELB improved by 0.402806
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.44
ELB improved by 0.420187
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.009
ELB improved by 0.431293
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.578
ELB improved by 0.430378
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.163
ELB improved by 0.415603
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.773
ELB improved by 0.39024
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.413
ELB improved by 0.359391
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.086
ELB improved by 0.327308
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.789
ELB improved by 0.29705
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.518
ELB improved by 0.271061
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.266
ELB improved by 0.252036
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.021
ELB improved by 0.244338
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.765
ELB improved by 0.25645
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.462
ELB improved by 0.302769
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.074
ELB improved by 0.388147
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.623
ELB improved by 0.451499
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.217
ELB improved by 0.405069
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.925
ELB improved by 0.292949
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.73
ELB improved by 0.194158
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.601
ELB improved by 0.128963
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.512
ELB improved by 0.0893102
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.447
ELB improved by 0.0646343
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.399
ELB improved by 0.0482654
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.362
ELB improved by 0.0367672
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.334
ELB improved by 0.0284228
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.312
ELB improved by 0.0222853
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.294
ELB improved by 0.017746
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.28
ELB improved by 0.0143715
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.268
ELB improved by 0.0118445
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.258
ELB improved by 0.00993365
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-873.186
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-595.922
ELB improved by 277.265
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-535.569
ELB improved by 60.3524
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.691
ELB improved by 45.8781
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.559
ELB improved by 24.1319
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.472
ELB improved by 10.0875
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.43
ELB improved by 5.04176
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.818
ELB improved by 3.61226
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.505
ELB improved by 3.31242
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.108
ELB improved by 3.39735
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.517
ELB improved by 3.5906
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.818
ELB improved by 3.69955
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.302
ELB improved by 3.51568
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.337
ELB improved by 2.96501
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.093
ELB improved by 2.24392
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.49
ELB improved by 1.60363
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.365
ELB improved by 1.1242
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.578
ELB improved by 0.787963
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.011
ELB improved by 0.566962
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.581
ELB improved by 0.429846
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.233
ELB improved by 0.347543
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.935
ELB improved by 0.298513
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.666
ELB improved by 0.268951
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.415
ELB improved by 0.250869
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.175
ELB improved by 0.239891
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.941
ELB improved by 0.233649
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.71
ELB improved by 0.23086
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.48
ELB improved by 0.23084
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.246
ELB improved by 0.233257
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.008
ELB improved by 0.238008
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.763
ELB improved by 0.245146
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.508
ELB improved by 0.254851
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.241
ELB improved by 0.267412
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.958
ELB improved by 0.283226
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.655
ELB improved by 0.302801
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.328
ELB improved by 0.326774
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.972
ELB improved by 0.355922
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.581
ELB improved by 0.391126
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.148
ELB improved by 0.43314
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.666
ELB improved by 0.481767
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.132
ELB improved by 0.533917
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.551
ELB improved by 0.581499
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.936
ELB improved by 0.614448
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.304
ELB improved by 0.631838
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.657
ELB improved by 0.647509
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.979
ELB improved by 0.67824
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.258
ELB improved by 0.720805
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.515
ELB improved by 0.743089
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.797
ELB improved by 0.717696
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.172
ELB improved by 0.625161
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.699
ELB improved by 0.472475
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.376
ELB improved by 0.323482
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.157
ELB improved by 0.219481
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.001
ELB improved by 0.155878
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.884
ELB improved by 0.116873
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.792
ELB improved by 0.0913639
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.719
ELB improved by 0.0734544
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.659
ELB improved by 0.0601913
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.609
ELB improved by 0.0500234
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.567
ELB improved by 0.0420551
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.531
ELB improved by 0.0357166
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.5
ELB improved by 0.0306186
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.474
ELB improved by 0.0264812
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.451
ELB improved by 0.0230969
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.43
ELB improved by 0.0203087
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.412
ELB improved by 0.0179956
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.396
ELB improved by 0.0160633
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.382
ELB improved by 0.0144375
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.369
ELB improved by 0.0130589
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.357
ELB improved by 0.0118799
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.346
ELB improved by 0.0108622
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.336
ELB improved by 0.00997503
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.055 0.096 1.179
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.029 | 0.007 | 0.036 | |
| getPIPs | 0.028 | 0.006 | 0.035 | |
| graper | 0.051 | 0.009 | 0.065 | |
| makeExampleData | 0.004 | 0.000 | 0.005 | |
| makeExampleDataWithUnequalGroups | 0.005 | 0.000 | 0.005 | |
| plotELBO | 0.131 | 0.009 | 0.148 | |
| plotGroupPenalties | 0.440 | 0.012 | 0.462 | |
| plotPosterior | 0.217 | 0.011 | 0.238 | |
| predict.graper | 1.027 | 0.037 | 1.078 | |
| print.graper | 0.027 | 0.005 | 0.032 | |