Britta Velten
| Snapshot Date: 2025-12-01 13:45 -0500 (Mon, 01 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_22 |
| git_last_commit: 76fc31b |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-04 12:02 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4624 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 922/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.26.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| 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: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2025-12-02 10:12:50 -0000 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 10:14:13 -0000 (Tue, 02 Dec 2025) |
| EllapsedTime: 83.1 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_1.26.0.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 ‘1.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘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 ‘1.26.0’ ** 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=-885.008
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.26
ELB improved by 300.748
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.766
ELB improved by 60.4936
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.802
ELB improved by 41.9648
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.472
ELB improved by 19.329
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.766
ELB improved by 7.7069
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.966
ELB improved by 3.79976
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.53
ELB improved by 2.43604
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.58
ELB improved by 1.94947
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.796
ELB improved by 1.78451
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.053
ELB improved by 1.74272
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.297
ELB improved by 1.75583
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.503
ELB improved by 1.79439
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.668
ELB improved by 1.83501
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.813
ELB improved by 1.85451
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.978
ELB improved by 1.83576
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.206
ELB improved by 1.77192
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.54
ELB improved by 1.6652
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.008
ELB improved by 1.5328
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.591
ELB improved by 1.41697
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.235
ELB improved by 1.3554
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.893
ELB improved by 1.34187
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.534
ELB improved by 1.35981
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.126
ELB improved by 1.40808
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.64
ELB improved by 1.48569
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.048
ELB improved by 1.59219
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.319
ELB improved by 1.72881
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.43
ELB improved by 1.88923
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.382
ELB improved by 2.04722
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.227
ELB improved by 2.15582
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.041
ELB improved by 2.18583
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.838
ELB improved by 2.20319
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.619
ELB improved by 2.21814
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.747
ELB improved by 1.87266
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.336
ELB improved by 1.41076
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.157
ELB improved by 1.17889
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.048
ELB improved by 1.10956
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.974
ELB improved by 1.07393
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.793
ELB improved by 1.18036
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.494
ELB improved by 1.29948
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.436
ELB improved by 1.05794
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.785
ELB improved by 0.650901
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.401
ELB improved by 0.383601
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.153
ELB improved by 0.248215
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.975
ELB improved by 0.177872
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.838
ELB improved by 0.136995
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.728
ELB improved by 0.110159
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.637
ELB improved by 0.0907864
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.561
ELB improved by 0.0759428
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.497
ELB improved by 0.0641777
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.443
ELB improved by 0.0546731
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.396
ELB improved by 0.0469071
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.355
ELB improved by 0.040515
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.32
ELB improved by 0.035227
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.289
ELB improved by 0.0308357
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.262
ELB improved by 0.0271786
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.238
ELB improved by 0.0241259
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.216
ELB improved by 0.0215731
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.197
ELB improved by 0.0194354
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.179
ELB improved by 0.0176435
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.163
ELB improved by 0.0161406
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.148
ELB improved by 0.0148799
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.134
ELB improved by 0.0138224
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.121
ELB improved by 0.0129359
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.109
ELB improved by 0.0121934
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.098
ELB improved by 0.011572
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.086
ELB improved by 0.0110522
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.076
ELB improved by 0.0106169
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.066
ELB improved by 0.0102512
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.056
ELB improved by 0.00994137
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-889.01
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-556.714
ELB improved by 332.296
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.048
ELB improved by 51.6659
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.057
ELB improved by 25.9914
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.4
ELB improved by 10.6563
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.84
ELB improved by 5.56039
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.676
ELB improved by 4.16404
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.903
ELB improved by 3.77343
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.238
ELB improved by 3.66447
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.707
ELB improved by 3.53128
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.472
ELB improved by 3.23482
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.693
ELB improved by 2.7785
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.455
ELB improved by 2.2389
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.791
ELB improved by 1.66362
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.657
ELB improved by 1.13366
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.906
ELB improved by 0.751243
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.385
ELB improved by 0.521257
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.993
ELB improved by 0.391801
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.674
ELB improved by 0.31933
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.395
ELB improved by 0.278628
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.139
ELB improved by 0.256207
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.894
ELB improved by 0.244913
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.653
ELB improved by 0.24093
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.411
ELB improved by 0.242188
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.163
ELB improved by 0.247509
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.907
ELB improved by 0.25616
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.639
ELB improved by 0.267615
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.358
ELB improved by 0.281419
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.061
ELB improved by 0.297115
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.747
ELB improved by 0.314191
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.415
ELB improved by 0.332071
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.065
ELB improved by 0.35012
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.697
ELB improved by 0.3677
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.313
ELB improved by 0.384264
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.913
ELB improved by 0.399471
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.5
ELB improved by 0.413265
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.074
ELB improved by 0.425856
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.636
ELB improved by 0.437627
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.187
ELB improved by 0.44904
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.727
ELB improved by 0.460655
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.253
ELB improved by 0.473414
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.764
ELB improved by 0.489206
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.253
ELB improved by 0.511388
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.71
ELB improved by 0.542993
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.132
ELB improved by 0.577444
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.54
ELB improved by 0.592438
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.952
ELB improved by 0.58744
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.346
ELB improved by 0.606618
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.68
ELB improved by 0.66623
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.98
ELB improved by 0.699371
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.331
ELB improved by 0.649007
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.82
ELB improved by 0.511437
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.472
ELB improved by 0.348015
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.239
ELB improved by 0.232278
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.075
ELB improved by 0.163921
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.953
ELB improved by 0.12222
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.859
ELB improved by 0.0944961
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.784
ELB improved by 0.0747368
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.724
ELB improved by 0.0600297
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.675
ELB improved by 0.0488114
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.635
ELB improved by 0.0401464
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.602
ELB improved by 0.0334132
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.573
ELB improved by 0.0281613
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.549
ELB improved by 0.0240469
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.529
ELB improved by 0.0208032
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.51
ELB improved by 0.018224
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.494
ELB improved by 0.0161515
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.48
ELB improved by 0.0144661
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.467
ELB improved by 0.0130781
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.455
ELB improved by 0.0119199
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.444
ELB improved by 0.0109412
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.434
ELB improved by 0.010104
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.424
ELB improved by 0.00937979
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.523
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.018
ELB improved by 290.505
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.64
ELB improved by 57.3786
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.218
ELB improved by 36.4219
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.715
ELB improved by 17.5029
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.563
ELB improved by 8.15204
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.263
ELB improved by 5.30019
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.252
ELB improved by 5.01084
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.741
ELB improved by 5.5104
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.578
ELB improved by 6.16382
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.253
ELB improved by 6.32491
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.813
ELB improved by 5.43944
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.975
ELB improved by 3.83832
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.561
ELB improved by 2.4135
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.022
ELB improved by 1.53956
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.963
ELB improved by 1.05852
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.201
ELB improved by 0.762376
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.638
ELB improved by 0.562857
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.203
ELB improved by 0.4346
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.847
ELB improved by 0.356
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.54
ELB improved by 0.307047
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.265
ELB improved by 0.27546
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.01
ELB improved by 0.254856
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.768
ELB improved by 0.241723
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.535
ELB improved by 0.233841
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.305
ELB improved by 0.229655
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.077
ELB improved by 0.228013
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.849
ELB improved by 0.228013
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.62
ELB improved by 0.228908
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.39
ELB improved by 0.23004
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.159
ELB improved by 0.230828
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.928
ELB improved by 0.230789
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.699
ELB improved by 0.229562
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.472
ELB improved by 0.226939
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.249
ELB improved by 0.22286
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.032
ELB improved by 0.2174
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.821
ELB improved by 0.210729
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.618
ELB improved by 0.203076
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.423
ELB improved by 0.194687
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.237
ELB improved by 0.185799
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.061
ELB improved by 0.176621
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.893
ELB improved by 0.167335
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.735
ELB improved by 0.158094
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.586
ELB improved by 0.149028
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.446
ELB improved by 0.140252
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.314
ELB improved by 0.131874
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.19
ELB improved by 0.123997
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.073
ELB improved by 0.116724
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.963
ELB improved by 0.110159
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.859
ELB improved by 0.104398
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.759
ELB improved by 0.0995241
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.664
ELB improved by 0.0955707
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.571
ELB improved by 0.092474
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.481
ELB improved by 0.0899972
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.394
ELB improved by 0.0876762
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.309
ELB improved by 0.0848669
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.228
ELB improved by 0.0809668
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.152
ELB improved by 0.0757233
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.083
ELB improved by 0.0693792
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.02
ELB improved by 0.0625044
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.964
ELB improved by 0.0556804
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.915
ELB improved by 0.0492986
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.872
ELB improved by 0.043539
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.833
ELB improved by 0.0384401
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.799
ELB improved by 0.0339707
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.769
ELB improved by 0.0300737
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.742
ELB improved by 0.0266871
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.719
ELB improved by 0.0237519
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.697
ELB improved by 0.0212142
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.678
ELB improved by 0.0190261
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.661
ELB improved by 0.017145
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.646
ELB improved by 0.015534
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.632
ELB improved by 0.0141612
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.619
ELB improved by 0.013
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.607
ELB improved by 0.0120284
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.595
ELB improved by 0.0112295
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.585
ELB improved by 0.0105912
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.575
ELB improved by 0.0101067
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.565
ELB improved by 0.009775
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-855.842
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-597.434
ELB improved by 258.408
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-537.547
ELB improved by 59.8868
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.892
ELB improved by 47.6555
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.475
ELB improved by 23.4166
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.056
ELB improved by 8.41889
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.228
ELB improved by 3.82795
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.52
ELB improved by 2.70823
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.102
ELB improved by 2.41819
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.752
ELB improved by 2.35018
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.407
ELB improved by 2.34502
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.076
ELB improved by 2.33073
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.812
ELB improved by 2.26373
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.692
ELB improved by 2.12035
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.789
ELB improved by 1.90296
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.172
ELB improved by 1.61661
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.911
ELB improved by 1.26126
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.996
ELB improved by 0.914516
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.335
ELB improved by 0.661326
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.832
ELB improved by 0.502843
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.425
ELB improved by 0.407586
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.076
ELB improved by 0.348813
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.766
ELB improved by 0.309908
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.484
ELB improved by 0.281529
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.226
ELB improved by 0.258621
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.987
ELB improved by 0.238563
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.767
ELB improved by 0.220123
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.564
ELB improved by 0.202843
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.378
ELB improved by 0.186651
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.206
ELB improved by 0.171628
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.048
ELB improved by 0.157876
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.903
ELB improved by 0.145469
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.768
ELB improved by 0.134427
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.644
ELB improved by 0.124717
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.527
ELB improved by 0.116263
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.418
ELB improved by 0.108958
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.316
ELB improved by 0.10268
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.218
ELB improved by 0.0973048
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.126
ELB improved by 0.092716
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.037
ELB improved by 0.0888086
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.951
ELB improved by 0.0854933
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.869
ELB improved by 0.0826965
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.788
ELB improved by 0.0803602
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.71
ELB improved by 0.0784406
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.633
ELB improved by 0.0769075
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.557
ELB improved by 0.0757432
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.482
ELB improved by 0.0749427
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.408
ELB improved by 0.0745145
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.333
ELB improved by 0.0744815
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.258
ELB improved by 0.0748832
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.183
ELB improved by 0.0757762
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.105
ELB improved by 0.077232
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.026
ELB improved by 0.0793243
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.944
ELB improved by 0.0820971
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.858
ELB improved by 0.0855009
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.769
ELB improved by 0.0893028
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.676
ELB improved by 0.0930283
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.58
ELB improved by 0.0960579
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.482
ELB improved by 0.0979438
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.383
ELB improved by 0.0987411
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.284
ELB improved by 0.0989895
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.185
ELB improved by 0.0993491
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.085
ELB improved by 0.100305
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.983
ELB improved by 0.102189
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.877
ELB improved by 0.105377
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.767
ELB improved by 0.110489
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.648
ELB improved by 0.118458
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.518
ELB improved by 0.130244
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.372
ELB improved by 0.145573
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.212
ELB improved by 0.160379
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.046
ELB improved by 0.165976
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.89
ELB improved by 0.155768
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.757
ELB improved by 0.133236
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.649
ELB improved by 0.107599
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.564
ELB improved by 0.0852076
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.496
ELB improved by 0.0678749
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.441
ELB improved by 0.0549908
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.396
ELB improved by 0.0453412
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.358
ELB improved by 0.0379009
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.326
ELB improved by 0.0319835
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.299
ELB improved by 0.0271654
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.276
ELB improved by 0.0231857
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.256
ELB improved by 0.0198744
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.239
ELB improved by 0.0171119
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.224
ELB improved by 0.0148061
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.211
ELB improved by 0.0128827
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.2
ELB improved by 0.0112791
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.19
ELB improved by 0.00994207
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.894 0.160 3.069
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.050 | 0.004 | 0.054 | |
| getPIPs | 0.048 | 0.000 | 0.049 | |
| graper | 0.069 | 0.008 | 0.077 | |
| makeExampleData | 0.008 | 0.000 | 0.009 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.000 | 0.010 | |
| plotELBO | 0.415 | 0.012 | 0.428 | |
| plotGroupPenalties | 1.509 | 0.032 | 1.544 | |
| plotPosterior | 0.919 | 0.016 | 0.937 | |
| predict.graper | 0.972 | 0.028 | 1.001 | |
| print.graper | 0.047 | 0.000 | 0.047 | |