Britta Velten
| Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 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 2025-10-21 12:07 -0400 (Tue, 21 Oct 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" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 918/2353 | 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 12.7.6 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: graper |
| Version: 1.25.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings graper_1.25.2.tar.gz |
| StartedAt: 2025-10-17 09:48:05 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 09:49:21 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 76.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings graper_1.25.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.8Mb
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.25.2’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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=-860.074
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.792
ELB improved by 319.282
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.068
ELB improved by 57.7239
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.57
ELB improved by 31.4981
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.552
ELB improved by 13.018
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.339
ELB improved by 6.21248
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.002
ELB improved by 4.3375
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.271
ELB improved by 3.73062
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.648
ELB improved by 3.62289
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.91
ELB improved by 3.73816
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.007
ELB improved by 3.90342
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.089
ELB improved by 3.91773
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.521
ELB improved by 3.56811
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.692
ELB improved by 2.82895
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.717
ELB improved by 1.97485
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.406
ELB improved by 1.31134
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.493
ELB improved by 0.912854
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.796
ELB improved by 0.696565
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.234
ELB improved by 0.562866
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.779
ELB improved by 0.454158
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.418
ELB improved by 0.36094
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.128
ELB improved by 0.290912
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.884
ELB improved by 0.243664
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.671
ELB improved by 0.212444
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.48
ELB improved by 0.19122
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.304
ELB improved by 0.176427
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.138
ELB improved by 0.166243
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.978
ELB improved by 0.159805
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.821
ELB improved by 0.15679
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.664
ELB improved by 0.157223
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.502
ELB improved by 0.161364
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.333
ELB improved by 0.169654
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.15
ELB improved by 0.18269
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.949
ELB improved by 0.201227
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.723
ELB improved by 0.226202
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.464
ELB improved by 0.258701
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.164
ELB improved by 0.299752
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.814
ELB improved by 0.349706
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.407
ELB improved by 0.407227
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.939
ELB improved by 0.46856
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.41
ELB improved by 0.528462
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.827
ELB improved by 0.583346
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.193
ELB improved by 0.634147
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.507
ELB improved by 0.685228
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.767
ELB improved by 0.740506
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.966
ELB improved by 0.801042
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.101
ELB improved by 0.864444
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.177
ELB improved by 0.924735
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.203
ELB improved by 0.974001
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.196
ELB improved by 1.00639
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.179
ELB improved by 1.017
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.189
ELB improved by 0.990569
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.284
ELB improved by 0.90471
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.522
ELB improved by 0.761624
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.926
ELB improved by 0.596077
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.48
ELB improved by 0.446588
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.149
ELB improved by 0.330611
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.905
ELB improved by 0.244075
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.726
ELB improved by 0.178866
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.595
ELB improved by 0.131431
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.496
ELB improved by 0.0991126
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.418
ELB improved by 0.078002
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.353
ELB improved by 0.0642673
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.298
ELB improved by 0.0551775
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.249
ELB improved by 0.0491004
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.204
ELB improved by 0.0451372
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.161
ELB improved by 0.0427682
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.12
ELB improved by 0.0415715
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.079
ELB improved by 0.0409841
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.039
ELB improved by 0.0401327
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.001
ELB improved by 0.0379226
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.967
ELB improved by 0.033604
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.94
ELB improved by 0.0275128
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.918
ELB improved by 0.0210342
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.903
ELB improved by 0.0155671
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.891
ELB improved by 0.0116673
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.882
ELB improved by 0.00913728
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-912.061
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-592.48
ELB improved by 319.581
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-532.205
ELB improved by 60.2754
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-496.797
ELB improved by 35.4078
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.901
ELB improved by 14.8963
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.828
ELB improved by 6.07264
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.413
ELB improved by 3.41503
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.931
ELB improved by 2.48238
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.777
ELB improved by 2.15338
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.751
ELB improved by 2.02595
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.785
ELB improved by 1.96592
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.864
ELB improved by 1.92131
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.008
ELB improved by 1.85627
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.265
ELB improved by 1.7429
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.691
ELB improved by 1.5739
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.32
ELB improved by 1.37081
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.155
ELB improved by 1.16527
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.188
ELB improved by 0.966447
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.416
ELB improved by 0.772088
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.816
ELB improved by 0.600374
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.345
ELB improved by 0.470557
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.962
ELB improved by 0.383149
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.634
ELB improved by 0.328512
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.337
ELB improved by 0.296305
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.059
ELB improved by 0.278679
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.788
ELB improved by 0.270512
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.52
ELB improved by 0.268743
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.248
ELB improved by 0.271649
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.97
ELB improved by 0.278337
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.681
ELB improved by 0.28839
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.38
ELB improved by 0.301621
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.062
ELB improved by 0.317856
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.725
ELB improved by 0.336782
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.367
ELB improved by 0.357976
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.986
ELB improved by 0.38117
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.579
ELB improved by 0.406588
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.144
ELB improved by 0.435006
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.677
ELB improved by 0.467434
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.172
ELB improved by 0.504637
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.625
ELB improved by 0.546697
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.033
ELB improved by 0.592659
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.392
ELB improved by 0.640339
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.706
ELB improved by 0.686593
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.977
ELB improved by 0.728599
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.211
ELB improved by 0.766477
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.406
ELB improved by 0.804321
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.571
ELB improved by 0.835569
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.76
ELB improved by 0.811053
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.069
ELB improved by 0.691181
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.535
ELB improved by 0.533817
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.131
ELB improved by 0.403442
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.819
ELB improved by 0.312335
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.571
ELB improved by 0.248068
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.376
ELB improved by 0.195365
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.228
ELB improved by 0.147878
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.12
ELB improved by 0.10804
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.041
ELB improved by 0.0782858
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.984
ELB improved by 0.0575749
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.94
ELB improved by 0.0434278
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.907
ELB improved by 0.0336703
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.88
ELB improved by 0.0268099
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.858
ELB improved by 0.0218891
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.84
ELB improved by 0.0182955
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.824
ELB improved by 0.0156301
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.81
ELB improved by 0.0136276
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.798
ELB improved by 0.0121082
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.787
ELB improved by 0.0109489
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.777
ELB improved by 0.0100646
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.768
ELB improved by 0.00939687
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-818.645
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-551.238
ELB improved by 267.408
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.145
ELB improved by 62.0924
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.915
ELB improved by 38.2301
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.717
ELB improved by 17.1984
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.714
ELB improved by 7.00265
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.124
ELB improved by 3.59002
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.622
ELB improved by 2.50206
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.491
ELB improved by 2.13136
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.383
ELB improved by 2.10802
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.079
ELB improved by 2.30384
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.43
ELB improved by 2.6483
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.372
ELB improved by 3.05865
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.97
ELB improved by 3.40133
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.453
ELB improved by 3.51731
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.159
ELB improved by 3.29394
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.411
ELB improved by 2.74768
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.33
ELB improved by 2.08154
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.812
ELB improved by 1.51842
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.659
ELB improved by 1.15218
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.697
ELB improved by 0.962458
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.806
ELB improved by 0.890404
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.941
ELB improved by 0.865878
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.104
ELB improved by 0.836808
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.297
ELB improved by 0.806431
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.507
ELB improved by 0.79031
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.722
ELB improved by 0.784629
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.942
ELB improved by 0.780683
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.168
ELB improved by 0.773835
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.405
ELB improved by 0.763012
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.657
ELB improved by 0.748291
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.928
ELB improved by 0.728919
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.225
ELB improved by 0.70253
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.559
ELB improved by 0.665769
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.943
ELB improved by 0.616028
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.39
ELB improved by 0.553392
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.908
ELB improved by 0.481491
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.502
ELB improved by 0.406449
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.167
ELB improved by 0.334641
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.897
ELB improved by 0.270745
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.68
ELB improved by 0.217021
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.506
ELB improved by 0.173676
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.366
ELB improved by 0.139674
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.253
ELB improved by 0.113494
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.159
ELB improved by 0.0936195
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.08
ELB improved by 0.0787689
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.012
ELB improved by 0.0679805
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.952
ELB improved by 0.0606192
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.895
ELB improved by 0.0563711
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.84
ELB improved by 0.0552322
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.783
ELB improved by 0.0574398
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.72
ELB improved by 0.0631443
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.648
ELB improved by 0.0714231
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.57
ELB improved by 0.0786558
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.491
ELB improved by 0.0787107
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.422
ELB improved by 0.0684402
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.37
ELB improved by 0.0524999
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.332
ELB improved by 0.0380495
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.304
ELB improved by 0.0280467
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.282
ELB improved by 0.0218832
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.264
ELB improved by 0.0182156
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.248
ELB improved by 0.0161041
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.233
ELB improved by 0.0150644
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.218
ELB improved by 0.0149205
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.202
ELB improved by 0.0157189
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.184
ELB improved by 0.0177259
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.163
ELB improved by 0.0214988
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.135
ELB improved by 0.0280139
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.096
ELB improved by 0.0387401
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.041
ELB improved by 0.0551962
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.964
ELB improved by 0.0769333
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.866
ELB improved by 0.097973
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.758
ELB improved by 0.10804
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.654
ELB improved by 0.103798
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.561
ELB improved by 0.0928212
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.478
ELB improved by 0.0831281
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.399
ELB improved by 0.0785069
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.319
ELB improved by 0.0804608
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.231
ELB improved by 0.08846
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.133
ELB improved by 0.097809
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.034
ELB improved by 0.0990296
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.948
ELB improved by 0.0858559
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.884
ELB improved by 0.0642574
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.839
ELB improved by 0.0447236
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.807
ELB improved by 0.0314317
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.784
ELB improved by 0.02332
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.766
ELB improved by 0.0183089
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.751
ELB improved by 0.014915
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.739
ELB improved by 0.0123346
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.728
ELB improved by 0.0102069
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.72
ELB improved by 0.00840556
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-868.393
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.247
ELB improved by 304.146
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.513
ELB improved by 58.7341
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.117
ELB improved by 32.3958
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.11
ELB improved by 14.0075
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.878
ELB improved by 6.23158
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.843
ELB improved by 4.03544
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.31
ELB improved by 3.53308
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.837
ELB improved by 3.47279
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.369
ELB improved by 3.46737
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.035
ELB improved by 3.33479
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.049
ELB improved by 2.98516
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.601
ELB improved by 2.44851
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.743
ELB improved by 1.85798
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.391
ELB improved by 1.35225
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.397
ELB improved by 0.993255
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.628
ELB improved by 0.769247
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.988
ELB improved by 0.640166
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.419
ELB improved by 0.56867
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.891
ELB improved by 0.528593
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.387
ELB improved by 0.503859
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.901
ELB improved by 0.485946
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.43
ELB improved by 0.470966
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.973
ELB improved by 0.45662
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.533
ELB improved by 0.440666
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.111
ELB improved by 0.421413
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.712
ELB improved by 0.398851
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.338
ELB improved by 0.37471
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.987
ELB improved by 0.351134
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.657
ELB improved by 0.329481
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.347
ELB improved by 0.310129
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.054
ELB improved by 0.292897
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.777
ELB improved by 0.277525
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.513
ELB improved by 0.264018
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.26
ELB improved by 0.252805
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.015
ELB improved by 0.24467
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.775
ELB improved by 0.240421
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.535
ELB improved by 0.239914
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.295
ELB improved by 0.240062
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.061
ELB improved by 0.233907
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.845
ELB improved by 0.216019
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.655
ELB improved by 0.190075
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.49
ELB improved by 0.164344
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.348
ELB improved by 0.142767
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.222
ELB improved by 0.125186
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.112
ELB improved by 0.110583
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.014
ELB improved by 0.0982071
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.926
ELB improved by 0.0875808
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.848
ELB improved by 0.0783784
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.777
ELB improved by 0.070357
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.714
ELB improved by 0.0633259
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.657
ELB improved by 0.0571314
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.605
ELB improved by 0.0516489
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.558
ELB improved by 0.0467772
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.516
ELB improved by 0.0424332
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.477
ELB improved by 0.038549
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.442
ELB improved by 0.035068
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.41
ELB improved by 0.0319427
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.381
ELB improved by 0.0291327
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.355
ELB improved by 0.0266036
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.33
ELB improved by 0.0243252
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.308
ELB improved by 0.0222713
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.288
ELB improved by 0.0204188
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.269
ELB improved by 0.0187472
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.252
ELB improved by 0.017238
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.236
ELB improved by 0.015875
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.221
ELB improved by 0.0146434
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.208
ELB improved by 0.0135302
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.195
ELB improved by 0.0125234
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.183
ELB improved by 0.0116123
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.173
ELB improved by 0.0107874
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.163
ELB improved by 0.01004
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.153
ELB improved by 0.00936233
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.810 0.181 2.984
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.050 | 0.004 | 0.055 | |
| getPIPs | 0.042 | 0.004 | 0.047 | |
| graper | 0.066 | 0.008 | 0.074 | |
| makeExampleData | 0.009 | 0.000 | 0.008 | |
| makeExampleDataWithUnequalGroups | 0.01 | 0.00 | 0.01 | |
| plotELBO | 0.410 | 0.016 | 0.428 | |
| plotGroupPenalties | 1.548 | 0.036 | 1.587 | |
| plotPosterior | 0.957 | 0.004 | 0.964 | |
| predict.graper | 1.021 | 0.024 | 1.047 | |
| print.graper | 0.048 | 0.000 | 0.048 | |