Britta Velten
| Snapshot Date: 2025-12-15 13:45 -0500 (Mon, 15 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 2025-12-18 12:07 -0500 (Thu, 18 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" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 922/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.26.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - 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: 2025-12-16 11:40:06 -0000 (Tue, 16 Dec 2025) |
| EndedAt: 2025-12-16 11:41:41 -0000 (Tue, 16 Dec 2025) |
| EllapsedTime: 94.1 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=-868.622
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.173
ELB improved by 295.449
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-518.664
ELB improved by 54.5088
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.486
ELB improved by 33.1785
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.175
ELB improved by 16.3103
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.491
ELB improved by 7.68416
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.564
ELB improved by 4.92661
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.054
ELB improved by 4.51015
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.272
ELB improved by 4.78276
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.301
ELB improved by 4.97009
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.716
ELB improved by 4.58567
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.08
ELB improved by 3.63561
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.477
ELB improved by 2.60323
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.611
ELB improved by 1.86568
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.186
ELB improved by 1.42527
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.08
ELB improved by 1.10578
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.273
ELB improved by 0.807522
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.718
ELB improved by 0.554609
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.34
ELB improved by 0.378128
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.07
ELB improved by 0.270488
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.863
ELB improved by 0.206376
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.697
ELB improved by 0.166154
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.558
ELB improved by 0.138939
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.439
ELB improved by 0.119172
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.335
ELB improved by 0.10398
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.243
ELB improved by 0.0918114
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.161
ELB improved by 0.0817745
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.088
ELB improved by 0.0733228
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.022
ELB improved by 0.0660986
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.962
ELB improved by 0.059854
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.908
ELB improved by 0.0544092
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.858
ELB improved by 0.0496283
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.813
ELB improved by 0.0454059
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.771
ELB improved by 0.0416579
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.733
ELB improved by 0.0383163
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.697
ELB improved by 0.0353255
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.665
ELB improved by 0.0326389
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.634
ELB improved by 0.0302179
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.606
ELB improved by 0.0280296
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.58
ELB improved by 0.0260463
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.556
ELB improved by 0.0242441
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.533
ELB improved by 0.0226027
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.512
ELB improved by 0.0211043
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.493
ELB improved by 0.0197336
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.474
ELB improved by 0.0184775
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.457
ELB improved by 0.0173241
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.441
ELB improved by 0.0162633
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.425
ELB improved by 0.0152861
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.411
ELB improved by 0.0143845
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.397
ELB improved by 0.0135515
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.385
ELB improved by 0.0127808
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.373
ELB improved by 0.012067
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.361
ELB improved by 0.0114049
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.35
ELB improved by 0.0107901
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.34
ELB improved by 0.0102186
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.33
ELB improved by 0.00968681
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-841.458
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.713
ELB improved by 256.745
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.781
ELB improved by 59.9324
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.799
ELB improved by 45.9819
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.231
ELB improved by 22.5676
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.152
ELB improved by 8.0788
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.442
ELB improved by 3.71034
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.823
ELB improved by 2.61859
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.434
ELB improved by 2.38966
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.99
ELB improved by 2.4438
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.358
ELB improved by 2.63199
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.416
ELB improved by 2.94232
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.001
ELB improved by 3.41411
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.919
ELB improved by 4.08267
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.088
ELB improved by 4.83032
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.905
ELB improved by 5.18382
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.306
ELB improved by 4.59858
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.008
ELB improved by 3.29821
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.945
ELB improved by 2.06268
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.679
ELB improved by 1.26595
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.838
ELB improved by 0.841545
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.2
ELB improved by 0.637352
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.651
ELB improved by 0.548935
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.13
ELB improved by 0.520935
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.604
ELB improved by 0.526443
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.052
ELB improved by 0.551716
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.465
ELB improved by 0.587667
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.839
ELB improved by 0.626143
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.179
ELB improved by 0.659713
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.495
ELB improved by 0.683346
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.8
ELB improved by 0.695615
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.102
ELB improved by 0.698114
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.408
ELB improved by 0.693696
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.723
ELB improved by 0.684824
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.05
ELB improved by 0.67274
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.393
ELB improved by 0.65744
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.755
ELB improved by 0.638278
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.14
ELB improved by 0.615057
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.55
ELB improved by 0.589975
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.978
ELB improved by 0.572125
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.386
ELB improved by 0.591185
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.664
ELB improved by 0.722664
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.711
ELB improved by 0.952469
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.774
ELB improved by 0.937741
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.046
ELB improved by 0.727337
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.502
ELB improved by 0.544339
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.086
ELB improved by 0.416149
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.754
ELB improved by 0.331432
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.477
ELB improved by 0.277755
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.232
ELB improved by 0.244162
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.012
ELB improved by 0.220753
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.813
ELB improved by 0.198738
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.639
ELB improved by 0.174007
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.49
ELB improved by 0.148421
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.365
ELB improved by 0.125396
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.259
ELB improved by 0.106465
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.167
ELB improved by 0.0915599
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.087
ELB improved by 0.0801835
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.015
ELB improved by 0.0719233
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.948
ELB improved by 0.0664512
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.885
ELB improved by 0.0633436
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.823
ELB improved by 0.0618544
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.763
ELB improved by 0.060716
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.704
ELB improved by 0.0582278
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.651
ELB improved by 0.0529971
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.606
ELB improved by 0.0450245
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.57
ELB improved by 0.0358677
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.543
ELB improved by 0.027438
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.522
ELB improved by 0.020806
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.506
ELB improved by 0.0160668
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.493
ELB improved by 0.0128273
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.483
ELB improved by 0.0106251
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.474
ELB improved by 0.0090989
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-922.588
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.933
ELB improved by 337.655
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-527.316
ELB improved by 57.6167
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-494.671
ELB improved by 32.6453
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.804
ELB improved by 13.8662
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.686
ELB improved by 6.11869
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.58
ELB improved by 4.10565
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.911
ELB improved by 3.66945
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.271
ELB improved by 3.64011
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.618
ELB improved by 3.65271
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.134
ELB improved by 3.48358
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.115
ELB improved by 3.01887
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.781
ELB improved by 2.33462
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.129
ELB improved by 1.65192
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.986
ELB improved by 1.14254
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.148
ELB improved by 0.838487
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.443
ELB improved by 0.704433
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.724
ELB improved by 0.719093
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.819
ELB improved by 0.905854
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.547
ELB improved by 1.27176
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.045
ELB improved by 1.50177
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.796
ELB improved by 1.24907
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.926
ELB improved by 0.870272
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.296
ELB improved by 0.629739
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.793
ELB improved by 0.503101
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.36
ELB improved by 0.432355
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.972
ELB improved by 0.38858
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.61
ELB improved by 0.361363
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.264
ELB improved by 0.346386
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.923
ELB improved by 0.340833
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.581
ELB improved by 0.342677
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.23
ELB improved by 0.350655
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.866
ELB improved by 0.364137
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.483
ELB improved by 0.382913
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.076
ELB improved by 0.406975
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.64
ELB improved by 0.436272
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.169
ELB improved by 0.470421
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.661
ELB improved by 0.508362
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.113
ELB improved by 0.548086
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.526
ELB improved by 0.586603
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.906
ELB improved by 0.620306
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.26
ELB improved by 0.645604
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.601
ELB improved by 0.659478
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.941
ELB improved by 0.65945
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.299
ELB improved by 0.642016
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.699
ELB improved by 0.600245
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.17
ELB improved by 0.529142
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.729
ELB improved by 0.441058
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.367
ELB improved by 0.361796
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.06
ELB improved by 0.307065
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.785
ELB improved by 0.274925
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.532
ELB improved by 0.252844
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.304
ELB improved by 0.228214
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.107
ELB improved by 0.197263
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.943
ELB improved by 0.163951
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.81
ELB improved by 0.133064
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.703
ELB improved by 0.107004
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.616
ELB improved by 0.0862538
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.546
ELB improved by 0.0703636
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.488
ELB improved by 0.0585336
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.438
ELB improved by 0.0499316
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.394
ELB improved by 0.043859
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.354
ELB improved by 0.0398175
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.316
ELB improved by 0.0375257
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.28
ELB improved by 0.0369295
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.241
ELB improved by 0.0382319
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.199
ELB improved by 0.0419544
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.15
ELB improved by 0.048994
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.09
ELB improved by 0.0605019
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.013
ELB improved by 0.0771126
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.916
ELB improved by 0.0971124
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.8
ELB improved by 0.115329
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.673
ELB improved by 0.127141
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.539
ELB improved by 0.133688
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.403
ELB improved by 0.135985
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.276
ELB improved by 0.127151
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.173
ELB improved by 0.103266
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.098
ELB improved by 0.0749334
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.044
ELB improved by 0.0540286
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.002
ELB improved by 0.0425954
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.964
ELB improved by 0.0378128
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.926
ELB improved by 0.0373572
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.886
ELB improved by 0.0405922
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.837
ELB improved by 0.0485416
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.773
ELB improved by 0.0642769
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.679
ELB improved by 0.0938293
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.534
ELB improved by 0.145249
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.317
ELB improved by 0.216835
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.043
ELB improved by 0.274497
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.762
ELB improved by 0.280064
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.506
ELB improved by 0.256619
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.27
ELB improved by 0.235529
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.066
ELB improved by 0.204347
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.911
ELB improved by 0.155412
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.803
ELB improved by 0.107995
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.728
ELB improved by 0.0748825
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.673
ELB improved by 0.0541792
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.633
ELB improved by 0.0407855
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.601
ELB improved by 0.031376
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.577
ELB improved by 0.0243697
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.558
ELB improved by 0.0190651
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.543
ELB improved by 0.0150804
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.531
ELB improved by 0.0121293
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.521
ELB improved by 0.00996658
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-885.253
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-598.022
ELB improved by 287.231
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-537.109
ELB improved by 60.9126
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.287
ELB improved by 45.8221
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.004
ELB improved by 24.2828
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.213
ELB improved by 9.79132
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.305
ELB improved by 4.90782
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.6
ELB improved by 3.70526
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.928
ELB improved by 3.67207
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.671
ELB improved by 4.25738
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.372
ELB improved by 5.29815
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.946
ELB improved by 6.42609
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.151
ELB improved by 6.79568
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.351
ELB improved by 5.79959
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.216
ELB improved by 4.13503
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.416
ELB improved by 2.79961
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.395
ELB improved by 2.02126
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.782
ELB improved by 1.61329
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.389
ELB improved by 1.39264
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.128
ELB improved by 1.2608
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.955
ELB improved by 1.17367
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.842
ELB improved by 1.11286
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.772
ELB improved by 1.06984
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.734
ELB improved by 1.03833
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.723
ELB improved by 1.01115
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.743
ELB improved by 0.979607
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.809
ELB improved by 0.934334
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.941
ELB improved by 0.867387
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.166
ELB improved by 0.775249
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.504
ELB improved by 0.66148
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.968
ELB improved by 0.536726
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.553
ELB improved by 0.415156
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.244
ELB improved by 0.309077
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.019
ELB improved by 0.224897
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.856
ELB improved by 0.162708
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.737
ELB improved by 0.118792
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.649
ELB improved by 0.0884437
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.581
ELB improved by 0.0675604
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.528
ELB improved by 0.0530897
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.485
ELB improved by 0.0429268
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.449
ELB improved by 0.0356685
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.419
ELB improved by 0.0303907
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.393
ELB improved by 0.0264857
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.369
ELB improved by 0.0235525
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.348
ELB improved by 0.021326
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.328
ELB improved by 0.0196312
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.31
ELB improved by 0.0183548
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.292
ELB improved by 0.017427
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.275
ELB improved by 0.0168117
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.259
ELB improved by 0.0165021
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.242
ELB improved by 0.0165224
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.226
ELB improved by 0.0169378
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.208
ELB improved by 0.0178763
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.188
ELB improved by 0.0195783
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.166
ELB improved by 0.0225026
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.138
ELB improved by 0.0275721
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.101
ELB improved by 0.0367765
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.046
ELB improved by 0.0547421
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.954
ELB improved by 0.092812
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.777
ELB improved by 0.177033
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.438
ELB improved by 0.338563
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.95
ELB improved by 0.488363
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.551
ELB improved by 0.398359
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.359
ELB improved by 0.192776
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.277
ELB improved by 0.0811228
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.234
ELB improved by 0.0430404
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.204
ELB improved by 0.030489
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.179
ELB improved by 0.0250213
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.157
ELB improved by 0.0215354
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.139
ELB improved by 0.0187391
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.122
ELB improved by 0.0163113
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.108
ELB improved by 0.0141812
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.096
ELB improved by 0.0123407
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.085
ELB improved by 0.0107864
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.075
ELB improved by 0.00950139
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.851 0.264 3.595
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.042 | 0.009 | 0.051 | |
| getPIPs | 0.047 | 0.000 | 0.048 | |
| graper | 0.069 | 0.004 | 0.074 | |
| makeExampleData | 0.008 | 0.000 | 0.009 | |
| makeExampleDataWithUnequalGroups | 0.009 | 0.000 | 0.010 | |
| plotELBO | 0.433 | 0.008 | 0.734 | |
| plotGroupPenalties | 1.570 | 0.048 | 2.242 | |
| plotPosterior | 1.006 | 0.008 | 1.183 | |
| predict.graper | 1.012 | 0.027 | 1.126 | |
| print.graper | 0.050 | 0.004 | 0.056 | |