Britta Velten
| Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_21 |
| git_last_commit: fb5f237 |
| git_last_commit_date: 2025-06-24 03:18:49 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-01 11:39 -0400 (Mon, 01 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 915/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.24.2 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.24.2 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings graper_1.24.2.tar.gz |
| StartedAt: 2025-08-31 23:05:08 -0400 (Sun, 31 Aug 2025) |
| EndedAt: 2025-08-31 23:06:31 -0400 (Sun, 31 Aug 2025) |
| EllapsedTime: 83.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings graper_1.24.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.24.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.24.2’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-912.105
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-598.929
ELB improved by 313.176
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.258
ELB improved by 58.6707
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.336
ELB improved by 44.9225
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.795
ELB improved by 23.5411
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.646
ELB improved by 10.1492
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.899
ELB improved by 5.74611
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.221
ELB improved by 4.67819
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.822
ELB improved by 4.39929
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.497
ELB improved by 4.32508
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.288
ELB improved by 4.20927
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.377
ELB improved by 3.91027
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.988
ELB improved by 3.38959
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.25
ELB improved by 2.73814
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.13
ELB improved by 2.11959
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.476
ELB improved by 1.65356
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.123
ELB improved by 1.35378
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.972
ELB improved by 1.15093
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.996
ELB improved by 0.975297
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.19
ELB improved by 0.806789
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.542
ELB improved by 0.647354
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.042
ELB improved by 0.500086
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.662
ELB improved by 0.380295
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.366
ELB improved by 0.295987
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.127
ELB improved by 0.239198
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.927
ELB improved by 0.199327
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.758
ELB improved by 0.16955
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.612
ELB improved by 0.146197
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.484
ELB improved by 0.12728
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.373
ELB improved by 0.111629
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.274
ELB improved by 0.0984957
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.187
ELB improved by 0.0873582
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.109
ELB improved by 0.0778355
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.039
ELB improved by 0.0696378
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.977
ELB improved by 0.0625388
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.921
ELB improved by 0.056359
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.87
ELB improved by 0.0509539
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.823
ELB improved by 0.046206
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.781
ELB improved by 0.0420189
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.743
ELB improved by 0.038313
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.708
ELB improved by 0.035022
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.676
ELB improved by 0.0320904
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.646
ELB improved by 0.0294713
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.619
ELB improved by 0.0271253
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.594
ELB improved by 0.0250184
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.571
ELB improved by 0.023122
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.55
ELB improved by 0.0214112
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.53
ELB improved by 0.0198645
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.511
ELB improved by 0.0184636
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.494
ELB improved by 0.0171923
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.478
ELB improved by 0.0160365
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.463
ELB improved by 0.014984
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.449
ELB improved by 0.0140239
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.436
ELB improved by 0.0131469
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.424
ELB improved by 0.0123444
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.412
ELB improved by 0.0116092
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.401
ELB improved by 0.0109346
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.391
ELB improved by 0.0103147
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.381
ELB improved by 0.00974443
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-866.327
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-574.766
ELB improved by 291.561
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.317
ELB improved by 59.4494
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.246
ELB improved by 42.0712
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.263
ELB improved by 17.983
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.366
ELB improved by 6.89626
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.514
ELB improved by 3.85199
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.522
ELB improved by 2.99267
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.744
ELB improved by 2.77772
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.921
ELB improved by 2.82316
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.914
ELB improved by 3.00706
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.642
ELB improved by 3.2721
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.075
ELB improved by 3.56647
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.281
ELB improved by 3.7943
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.493
ELB improved by 3.78846
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.103
ELB improved by 3.38926
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.465
ELB improved by 2.63796
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.64
ELB improved by 1.82493
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.43
ELB improved by 1.21005
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.593
ELB improved by 0.837074
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.959
ELB improved by 0.634113
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.431
ELB improved by 0.527787
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.959
ELB improved by 0.472682
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.514
ELB improved by 0.444543
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.084
ELB improved by 0.430575
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.66
ELB improved by 0.423675
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.24
ELB improved by 0.419648
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.824
ELB improved by 0.415973
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.413
ELB improved by 0.41129
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.008
ELB improved by 0.405162
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.61
ELB improved by 0.397933
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.219
ELB improved by 0.390626
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.834
ELB improved by 0.384947
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.451
ELB improved by 0.383519
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.06
ELB improved by 0.39031
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.65
ELB improved by 0.410117
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.208
ELB improved by 0.44277
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.736
ELB improved by 0.471416
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.262
ELB improved by 0.473699
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.806
ELB improved by 0.45657
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.366
ELB improved by 0.439489
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.939
ELB improved by 0.427871
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.518
ELB improved by 0.420457
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.101
ELB improved by 0.41726
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.679
ELB improved by 0.422032
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.231
ELB improved by 0.447494
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.695
ELB improved by 0.536528
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.882
ELB improved by 0.813069
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.629
ELB improved by 1.25278
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.362
ELB improved by 1.2668
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.32
ELB improved by 1.04225
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.425
ELB improved by 0.894551
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.56
ELB improved by 0.865549
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.637
ELB improved by 0.922478
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.794
ELB improved by 0.842839
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.178
ELB improved by 0.616868
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.743
ELB improved by 0.434907
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.422
ELB improved by 0.320594
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.176
ELB improved by 0.246348
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.982
ELB improved by 0.193739
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.828
ELB improved by 0.153992
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.705
ELB improved by 0.123167
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.606
ELB improved by 0.0991993
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.525
ELB improved by 0.0807168
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.458
ELB improved by 0.0666765
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.402
ELB improved by 0.0562584
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.353
ELB improved by 0.048834
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.309
ELB improved by 0.0439475
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.268
ELB improved by 0.04129
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.227
ELB improved by 0.040656
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.185
ELB improved by 0.0418696
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.141
ELB improved by 0.0446801
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.092
ELB improved by 0.0486534
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.039
ELB improved by 0.0531431
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.981
ELB improved by 0.0574403
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.92
ELB improved by 0.0610871
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.856
ELB improved by 0.0641649
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.789
ELB improved by 0.067352
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.717
ELB improved by 0.0717068
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.639
ELB improved by 0.0781383
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.553
ELB improved by 0.086374
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.459
ELB improved by 0.0936031
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.365
ELB improved by 0.0945118
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.28
ELB improved by 0.0850302
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.212
ELB improved by 0.0671709
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.165
ELB improved by 0.0477278
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.133
ELB improved by 0.0320395
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.111
ELB improved by 0.0213673
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.097
ELB improved by 0.0146916
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.086
ELB improved by 0.0106429
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.078
ELB improved by 0.00819086
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.32
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.438
ELB improved by 283.882
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.852
ELB improved by 61.5861
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.025
ELB improved by 38.8269
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.659
ELB improved by 17.3664
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.82
ELB improved by 7.83891
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.774
ELB improved by 5.04561
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.435
ELB improved by 4.33921
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.063
ELB improved by 4.37187
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.463
ELB improved by 4.60039
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.799
ELB improved by 4.66338
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.563
ELB improved by 4.2364
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.241
ELB improved by 3.32139
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.937
ELB improved by 2.30492
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.413
ELB improved by 1.52306
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.385
ELB improved by 1.02854
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.649
ELB improved by 0.735702
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.09
ELB improved by 0.559426
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.643
ELB improved by 0.44692
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.273
ELB improved by 0.369871
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.959
ELB improved by 0.31361
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.689
ELB improved by 0.270279
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.454
ELB improved by 0.235347
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.248
ELB improved by 0.206051
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.067
ELB improved by 0.180746
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.908
ELB improved by 0.158571
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.769
ELB improved by 0.139157
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.647
ELB improved by 0.122327
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.539
ELB improved by 0.107902
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.443
ELB improved by 0.0956284
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.358
ELB improved by 0.0852055
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.282
ELB improved by 0.0763294
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.213
ELB improved by 0.0687285
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.151
ELB improved by 0.0621755
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.094
ELB improved by 0.056487
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.043
ELB improved by 0.0515168
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.996
ELB improved by 0.0471489
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.953
ELB improved by 0.0432903
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.913
ELB improved by 0.0398658
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.876
ELB improved by 0.0368139
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.842
ELB improved by 0.0340842
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.81
ELB improved by 0.0316343
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.781
ELB improved by 0.0294289
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.753
ELB improved by 0.0274378
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.728
ELB improved by 0.0256356
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.704
ELB improved by 0.0240003
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.681
ELB improved by 0.0225129
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.66
ELB improved by 0.0211571
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.64
ELB improved by 0.0199186
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.621
ELB improved by 0.0187851
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.604
ELB improved by 0.0177455
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.587
ELB improved by 0.0167904
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.571
ELB improved by 0.0159113
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.556
ELB improved by 0.0151007
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.541
ELB improved by 0.014352
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.528
ELB improved by 0.0136592
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.515
ELB improved by 0.0130173
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.502
ELB improved by 0.0124214
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.49
ELB improved by 0.0118675
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.479
ELB improved by 0.0113518
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.468
ELB improved by 0.010871
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.458
ELB improved by 0.0104219
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.448
ELB improved by 0.010002
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.438
ELB improved by 0.00960883
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-846.746
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.942
ELB improved by 259.804
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.099
ELB improved by 61.8432
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.009
ELB improved by 50.09
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.194
ELB improved by 28.8151
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.503
ELB improved by 12.6904
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.326
ELB improved by 6.1776
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.028
ELB improved by 4.29787
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.382
ELB improved by 3.6458
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.998
ELB improved by 3.38422
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.728
ELB improved by 3.26995
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.523
ELB improved by 3.20479
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.406
ELB improved by 3.11724
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.478
ELB improved by 2.92834
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.89
ELB improved by 2.58781
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.753
ELB improved by 2.13642
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.074
ELB improved by 1.67889
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.798
ELB improved by 1.27595
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.86
ELB improved by 0.938171
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.179
ELB improved by 0.681051
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.672
ELB improved by 0.507623
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.273
ELB improved by 0.39831
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.943
ELB improved by 0.329859
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.658
ELB improved by 0.285851
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.401
ELB improved by 0.256762
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.163
ELB improved by 0.237531
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.937
ELB improved by 0.225801
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.716
ELB improved by 0.221127
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.491
ELB improved by 0.224888
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.251
ELB improved by 0.240571
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.978
ELB improved by 0.273375
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.651
ELB improved by 0.326037
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.264
ELB improved by 0.387304
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.838
ELB improved by 0.426403
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.413
ELB improved by 0.425143
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.009
ELB improved by 0.403315
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.627
ELB improved by 0.382359
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.262
ELB improved by 0.365422
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.912
ELB improved by 0.350002
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.576
ELB improved by 0.335089
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.256
ELB improved by 0.320908
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.948
ELB improved by 0.30773
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.652
ELB improved by 0.295376
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.369
ELB improved by 0.283245
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.099
ELB improved by 0.270562
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.842
ELB improved by 0.256657
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.601
ELB improved by 0.241174
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.377
ELB improved by 0.224147
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.171
ELB improved by 0.205957
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.983
ELB improved by 0.187228
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.815
ELB improved by 0.168695
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.664
ELB improved by 0.151096
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.529
ELB improved by 0.135084
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.407
ELB improved by 0.121211
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.297
ELB improved by 0.109968
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.195
ELB improved by 0.101929
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.097
ELB improved by 0.098071
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.997
ELB improved by 0.100443
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.883
ELB improved by 0.113614
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.736
ELB improved by 0.147083
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.523
ELB improved by 0.213313
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.226
ELB improved by 0.296682
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.908
ELB improved by 0.31866
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.65
ELB improved by 0.257248
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.467
ELB improved by 0.183236
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.337
ELB improved by 0.129954
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.242
ELB improved by 0.0952172
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.169
ELB improved by 0.0724585
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.112
ELB improved by 0.0571829
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.066
ELB improved by 0.0466986
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.026
ELB improved by 0.0393858
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.992
ELB improved by 0.034239
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.961
ELB improved by 0.0306211
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.933
ELB improved by 0.0281291
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.907
ELB improved by 0.026514
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.881
ELB improved by 0.025628
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.856
ELB improved by 0.0253842
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.83
ELB improved by 0.0257153
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.803
ELB improved by 0.0265218
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.776
ELB improved by 0.0276059
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.747
ELB improved by 0.0286135
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.718
ELB improved by 0.0290486
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.69
ELB improved by 0.0284321
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.663
ELB improved by 0.0265708
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.639
ELB improved by 0.0237236
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.619
ELB improved by 0.0204687
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.602
ELB improved by 0.0173797
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.587
ELB improved by 0.0147964
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.574
ELB improved by 0.0128095
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.563
ELB improved by 0.0113633
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.552
ELB improved by 0.0103573
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.543
ELB improved by 0.0097032
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.243 0.193 2.424
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.054 | 0.016 | 0.071 | |
| getPIPs | 0.049 | 0.016 | 0.064 | |
| graper | 0.081 | 0.022 | 0.103 | |
| makeExampleData | 0.009 | 0.002 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.029 | 0.011 | 0.040 | |
| plotELBO | 0.196 | 0.022 | 0.219 | |
| plotGroupPenalties | 0.688 | 0.017 | 0.705 | |
| plotPosterior | 0.476 | 0.009 | 0.484 | |
| predict.graper | 2.061 | 0.061 | 2.125 | |
| print.graper | 0.055 | 0.009 | 0.064 | |