Britta Velten
| Snapshot Date: 2025-09-29 13:40 -0400 (Mon, 29 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_21 |
| git_last_commit: fb5f237 |
| git_last_commit_date: 2025-06-24 03:18:49 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-02 11:41 -0400 (Thu, 02 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4831 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4612 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4584 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 915/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.24.2 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: graper |
| Version: 1.24.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings graper_1.24.2.tar.gz |
| StartedAt: 2025-09-30 10:19:40 -0000 (Tue, 30 Sep 2025) |
| EndedAt: 2025-09-30 10:20:48 -0000 (Tue, 30 Sep 2025) |
| EllapsedTime: 68.0 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_1.24.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.24.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘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-3.21-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-devel_2025-02-19/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.24.2’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -L/home/biocbuild/R/R/lib -lRlapack -L/home/biocbuild/R/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-devel_2025-02-19/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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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=-882.421
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-565.461
ELB improved by 316.96
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-502.362
ELB improved by 63.0991
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.448
ELB improved by 35.9143
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.866
ELB improved by 14.5817
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.061
ELB improved by 6.80563
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.281
ELB improved by 4.77934
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.922
ELB improved by 4.35908
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.495
ELB improved by 4.42677
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.876
ELB improved by 4.61912
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.204
ELB improved by 4.67209
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.868
ELB improved by 4.33631
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.315
ELB improved by 3.55297
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.742
ELB improved by 2.57324
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.997
ELB improved by 1.74438
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.788
ELB improved by 1.20927
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.882
ELB improved by 0.906051
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.161
ELB improved by 0.720822
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.577
ELB improved by 0.583817
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.094
ELB improved by 0.483061
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.674
ELB improved by 0.420228
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.286
ELB improved by 0.388071
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.908
ELB improved by 0.377617
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.525
ELB improved by 0.383612
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.12
ELB improved by 0.404432
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.679
ELB improved by 0.440883
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.184
ELB improved by 0.495268
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.613
ELB improved by 0.570656
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.943
ELB improved by 0.670073
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.148
ELB improved by 0.795315
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.203
ELB improved by 0.94527
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.088
ELB improved by 1.11468
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.793
ELB improved by 1.29489
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.32
ELB improved by 1.47353
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.692
ELB improved by 1.62755
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.975
ELB improved by 1.71731
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.277
ELB improved by 1.69758
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.731
ELB improved by 1.54588
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.445
ELB improved by 1.28644
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.461
ELB improved by 0.98403
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.754
ELB improved by 0.706549
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.264
ELB improved by 0.490835
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.924
ELB improved by 0.339574
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.685
ELB improved by 0.239032
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.511
ELB improved by 0.173924
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.379
ELB improved by 0.131987
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.275
ELB improved by 0.104272
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.19
ELB improved by 0.0849861
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.119
ELB improved by 0.0709022
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.059
ELB improved by 0.0603598
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.006
ELB improved by 0.0523958
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.96
ELB improved by 0.0462893
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.918
ELB improved by 0.0414346
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.881
ELB improved by 0.0373485
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.847
ELB improved by 0.0336926
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.817
ELB improved by 0.0302736
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.79
ELB improved by 0.0270205
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.766
ELB improved by 0.0239456
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.745
ELB improved by 0.0210997
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.726
ELB improved by 0.0185342
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.71
ELB improved by 0.0162784
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.696
ELB improved by 0.0143337
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.683
ELB improved by 0.0126791
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.672
ELB improved by 0.0112808
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.662
ELB improved by 0.0101004
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.653
ELB improved by 0.00910148
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-875.511
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.003
ELB improved by 304.507
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.558
ELB improved by 64.445
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.523
ELB improved by 33.0351
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.206
ELB improved by 13.3176
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.973
ELB improved by 6.2322
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.866
ELB improved by 4.10719
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.411
ELB improved by 3.45522
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.09
ELB improved by 3.32082
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.729
ELB improved by 3.36111
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.378
ELB improved by 3.35157
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.276
ELB improved by 3.10129
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.73
ELB improved by 2.54642
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.889
ELB improved by 1.84062
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.67
ELB improved by 1.21888
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.878
ELB improved by 0.792669
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.34
ELB improved by 0.538089
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.947
ELB improved by 0.392106
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.641
ELB improved by 0.306591
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.387
ELB improved by 0.253901
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.168
ELB improved by 0.219416
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.972
ELB improved by 0.195457
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.794
ELB improved by 0.177919
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.63
ELB improved by 0.164534
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.476
ELB improved by 0.153988
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.33
ELB improved by 0.145469
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.192
ELB improved by 0.138442
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.059
ELB improved by 0.13253
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.932
ELB improved by 0.127451
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.809
ELB improved by 0.122985
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.69
ELB improved by 0.118962
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.575
ELB improved by 0.115243
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.463
ELB improved by 0.11172
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.355
ELB improved by 0.108311
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.25
ELB improved by 0.104954
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.148
ELB improved by 0.10161
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.05
ELB improved by 0.0982565
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.955
ELB improved by 0.0948861
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.863
ELB improved by 0.0915037
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.775
ELB improved by 0.0881236
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.69
ELB improved by 0.0847665
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.609
ELB improved by 0.0814572
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.531
ELB improved by 0.0782216
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.456
ELB improved by 0.0750858
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.384
ELB improved by 0.0720739
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.314
ELB improved by 0.069208
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.248
ELB improved by 0.0665073
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.184
ELB improved by 0.0639888
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.122
ELB improved by 0.0616671
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.063
ELB improved by 0.0595554
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.005
ELB improved by 0.0576665
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.949
ELB improved by 0.0560137
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.894
ELB improved by 0.0546126
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.841
ELB improved by 0.0534822
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.788
ELB improved by 0.0526475
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.736
ELB improved by 0.0521427
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.684
ELB improved by 0.0520152
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.632
ELB improved by 0.0523323
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.579
ELB improved by 0.0531908
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.524
ELB improved by 0.0547335
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.467
ELB improved by 0.057174
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.406
ELB improved by 0.0608408
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.34
ELB improved by 0.066249
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.265
ELB improved by 0.0742192
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.179
ELB improved by 0.0860555
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.076
ELB improved by 0.103735
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.946
ELB improved by 0.129815
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.78
ELB improved by 0.166163
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.569
ELB improved by 0.210458
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.316
ELB improved by 0.253228
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.032
ELB improved by 0.283541
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.733
ELB improved by 0.299081
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.429
ELB improved by 0.304208
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.127
ELB improved by 0.302372
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.832
ELB improved by 0.294729
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.55
ELB improved by 0.281726
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.286
ELB improved by 0.263985
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.044
ELB improved by 0.24254
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.825
ELB improved by 0.218823
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.63
ELB improved by 0.1945
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.459
ELB improved by 0.171193
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.309
ELB improved by 0.150234
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.176
ELB improved by 0.132532
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.058
ELB improved by 0.118569
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.949
ELB improved by 0.108501
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.847
ELB improved by 0.102314
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.747
ELB improved by 0.100049
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.645
ELB improved by 0.102112
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.535
ELB improved by 0.109445
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.413
ELB improved by 0.122688
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.274
ELB improved by 0.138973
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.125
ELB improved by 0.148926
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.981
ELB improved by 0.143724
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.854
ELB improved by 0.127082
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.745
ELB improved by 0.108748
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.653
ELB improved by 0.0921002
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.577
ELB improved by 0.0758228
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.518
ELB improved by 0.0596081
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.473
ELB improved by 0.0449772
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.439
ELB improved by 0.0333116
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.415
ELB improved by 0.0248254
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.396
ELB improved by 0.0189437
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.381
ELB improved by 0.0149204
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.369
ELB improved by 0.0121412
iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.358
ELB improved by 0.0101773
iteration 106
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.35
ELB improved by 0.00875002
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-882.062
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-572.506
ELB improved by 309.556
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.918
ELB improved by 57.5879
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.292
ELB improved by 34.6255
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.862
ELB improved by 14.4301
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.601
ELB improved by 6.26099
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.548
ELB improved by 4.05318
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.005
ELB improved by 3.54327
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.389
ELB improved by 3.61533
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.52
ELB improved by 3.86988
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.531
ELB improved by 3.98878
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.836
ELB improved by 3.69467
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.836
ELB improved by 2.99964
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.592
ELB improved by 2.24408
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.869
ELB improved by 1.72345
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.396
ELB improved by 1.47306
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.02
ELB improved by 1.37606
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.703
ELB improved by 1.31662
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.442
ELB improved by 1.26158
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.227
ELB improved by 1.2146
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.051
ELB improved by 1.17599
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.904
ELB improved by 1.14686
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.774
ELB improved by 1.13063
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.643
ELB improved by 1.1306
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.495
ELB improved by 1.148
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.314
ELB improved by 1.18099
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.092
ELB improved by 1.22225
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.837
ELB improved by 1.25437
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.589
ELB improved by 1.24839
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.414
ELB improved by 1.1753
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.383
ELB improved by 1.03055
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.534
ELB improved by 0.849177
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.841
ELB improved by 0.692597
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.213
ELB improved by 0.627826
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.515
ELB improved by 0.698715
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.751
ELB improved by 0.763302
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.128
ELB improved by 0.623659
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.67
ELB improved by 0.457983
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.25
ELB improved by 0.420218
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.748
ELB improved by 0.501949
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.288
ELB improved by 0.45921
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.041
ELB improved by 0.247232
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.929
ELB improved by 0.111896
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.87
ELB improved by 0.0589366
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.832
ELB improved by 0.0385689
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.802
ELB improved by 0.0295584
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.778
ELB improved by 0.0246844
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.756
ELB improved by 0.0214713
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.737
ELB improved by 0.0190373
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.72
ELB improved by 0.017048
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.705
ELB improved by 0.015361
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.691
ELB improved by 0.0139043
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.678
ELB improved by 0.0126343
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.667
ELB improved by 0.0115202
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.656
ELB improved by 0.0105387
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.646
ELB improved by 0.00967097
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-860.748
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.589
ELB improved by 274.16
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.352
ELB improved by 60.2362
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.456
ELB improved by 44.8962
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.751
ELB improved by 22.7047
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.049
ELB improved by 10.7025
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.762
ELB improved by 7.2868
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.012
ELB improved by 6.7499
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.136
ELB improved by 6.87592
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.523
ELB improved by 6.61338
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.91
ELB improved by 5.61318
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.717
ELB improved by 4.19304
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.809
ELB improved by 2.90795
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.767
ELB improved by 2.04215
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.211
ELB improved by 1.55521
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.931
ELB improved by 1.27994
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.854
ELB improved by 1.07772
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.917
ELB improved by 0.936822
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.049
ELB improved by 0.867962
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.247
ELB improved by 0.801482
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.525
ELB improved by 0.722869
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.903
ELB improved by 0.621669
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.454
ELB improved by 0.448439
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.161
ELB improved by 0.293008
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.955
ELB improved by 0.206422
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.794
ELB improved by 0.160794
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.661
ELB improved by 0.132762
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.549
ELB improved by 0.11283
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.451
ELB improved by 0.0974098
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.366
ELB improved by 0.0849608
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.292
ELB improved by 0.0746781
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.226
ELB improved by 0.0660626
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.167
ELB improved by 0.0587689
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.114
ELB improved by 0.0525426
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.067
ELB improved by 0.0471894
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.024
ELB improved by 0.0425581
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.986
ELB improved by 0.0385285
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.951
ELB improved by 0.0350044
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.919
ELB improved by 0.0319079
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.89
ELB improved by 0.0291752
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.863
ELB improved by 0.0267538
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.839
ELB improved by 0.0246002
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.816
ELB improved by 0.0226781
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.795
ELB improved by 0.0209568
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.775
ELB improved by 0.0194108
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.757
ELB improved by 0.018018
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.741
ELB improved by 0.0167598
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.725
ELB improved by 0.0156203
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.71
ELB improved by 0.0145856
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.697
ELB improved by 0.013644
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.684
ELB improved by 0.0127851
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.672
ELB improved by 0.012
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.661
ELB improved by 0.0112808
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.65
ELB improved by 0.0106208
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.64
ELB improved by 0.010014
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.631
ELB improved by 0.00945504
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.817 0.160 2.970
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.077 | 0.012 | 0.090 | |
| getPIPs | 0.081 | 0.000 | 0.081 | |
| graper | 0.126 | 0.004 | 0.131 | |
| makeExampleData | 0.014 | 0.000 | 0.013 | |
| makeExampleDataWithUnequalGroups | 0.036 | 0.000 | 0.035 | |
| plotELBO | 0.277 | 0.008 | 0.286 | |
| plotGroupPenalties | 0.988 | 0.007 | 1.001 | |
| plotPosterior | 0.784 | 0.004 | 0.789 | |
| predict.graper | 3.095 | 0.020 | 3.126 | |
| print.graper | 0.078 | 0.004 | 0.083 | |