Britta Velten
| Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 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 2025-09-25 11:42 -0400 (Thu, 25 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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: 2025-09-23 10:32:28 -0000 (Tue, 23 Sep 2025) |
| EndedAt: 2025-09-23 10:33:38 -0000 (Tue, 23 Sep 2025) |
| EllapsedTime: 69.1 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_1.24.2.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=-879.358
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-602.342
ELB improved by 277.016
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-543.336
ELB improved by 59.0062
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.641
ELB improved by 45.6951
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.999
ELB improved by 24.6413
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.98
ELB improved by 10.0194
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.502
ELB improved by 4.47786
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.449
ELB improved by 3.05349
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.933
ELB improved by 2.51579
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.656
ELB improved by 2.2768
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.505
ELB improved by 2.15083
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.458
ELB improved by 2.04742
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.53
ELB improved by 1.92743
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.754
ELB improved by 1.7764
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.157
ELB improved by 1.59734
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.751
ELB improved by 1.40525
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.537
ELB improved by 1.21468
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.509
ELB improved by 1.02821
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.666
ELB improved by 0.842563
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.001
ELB improved by 0.665322
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.487
ELB improved by 0.513243
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.092
ELB improved by 0.395676
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.783
ELB improved by 0.309193
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.538
ELB improved by 0.244973
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.342
ELB improved by 0.195863
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.184
ELB improved by 0.157975
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.055
ELB improved by 0.129119
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.947
ELB improved by 0.107428
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.856
ELB improved by 0.0911171
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.777
ELB improved by 0.078691
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.708
ELB improved by 0.0690348
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.647
ELB improved by 0.0613653
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.592
ELB improved by 0.0551417
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.542
ELB improved by 0.0499892
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.496
ELB improved by 0.0456448
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.454
ELB improved by 0.0419218
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.416
ELB improved by 0.0386857
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.38
ELB improved by 0.0358388
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.346
ELB improved by 0.0333085
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.315
ELB improved by 0.0310406
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.286
ELB improved by 0.0289936
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.259
ELB improved by 0.0271354
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.234
ELB improved by 0.0254405
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.21
ELB improved by 0.0238884
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.187
ELB improved by 0.0224624
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.166
ELB improved by 0.0211486
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.146
ELB improved by 0.0199353
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.128
ELB improved by 0.0188124
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.11
ELB improved by 0.0177712
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.093
ELB improved by 0.0168042
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.077
ELB improved by 0.0159048
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.062
ELB improved by 0.0150672
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.048
ELB improved by 0.014286
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.034
ELB improved by 0.0135566
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.021
ELB improved by 0.0128749
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.009
ELB improved by 0.012237
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.997
ELB improved by 0.0116396
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.986
ELB improved by 0.0110795
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.976
ELB improved by 0.010554
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.966
ELB improved by 0.0100605
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.956
ELB improved by 0.00959671
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-893.416
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-587.004
ELB improved by 306.412
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-529.157
ELB improved by 57.8475
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.251
ELB improved by 39.9059
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.846
ELB improved by 19.4045
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.602
ELB improved by 8.24461
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.654
ELB improved by 4.94771
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.749
ELB improved by 3.90468
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.213
ELB improved by 3.53601
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.802
ELB improved by 3.41139
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.441
ELB improved by 3.36097
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.16
ELB improved by 3.28048
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.087
ELB improved by 3.07305
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.404
ELB improved by 2.68285
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.263
ELB improved by 2.14164
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.695
ELB improved by 1.5674
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.602
ELB improved by 1.09375
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.828
ELB improved by 0.773927
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.246
ELB improved by 0.58189
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.774
ELB improved by 0.471774
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.365
ELB improved by 0.408996
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.992
ELB improved by 0.372974
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.64
ELB improved by 0.35235
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.299
ELB improved by 0.340928
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.963
ELB improved by 0.335336
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.63
ELB improved by 0.333893
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.293
ELB improved by 0.336247
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.95
ELB improved by 0.343484
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.591
ELB improved by 0.358418
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.206
ELB improved by 0.384969
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.783
ELB improved by 0.423416
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.323
ELB improved by 0.45992
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.853
ELB improved by 0.470061
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.397
ELB improved by 0.456216
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.943
ELB improved by 0.454193
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.465
ELB improved by 0.477577
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.986
ELB improved by 0.479214
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.563
ELB improved by 0.422751
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.213
ELB improved by 0.35041
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.925
ELB improved by 0.287923
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.686
ELB improved by 0.23833
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.485
ELB improved by 0.201076
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.313
ELB improved by 0.172822
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.162
ELB improved by 0.150409
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.03
ELB improved by 0.131902
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.914
ELB improved by 0.116255
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.811
ELB improved by 0.102886
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.72
ELB improved by 0.0914359
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.638
ELB improved by 0.0816456
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.565
ELB improved by 0.0733105
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.498
ELB improved by 0.0662589
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.438
ELB improved by 0.0603461
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.383
ELB improved by 0.0554511
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.331
ELB improved by 0.0514774
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.283
ELB improved by 0.0483526
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.237
ELB improved by 0.0460289
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.192
ELB improved by 0.0444814
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.149
ELB improved by 0.0437033
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.105
ELB improved by 0.0436933
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.06
ELB improved by 0.044431
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.015
ELB improved by 0.0458346
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.967
ELB improved by 0.0477066
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.917
ELB improved by 0.0496938
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.866
ELB improved by 0.0513189
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.814
ELB improved by 0.0521241
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.762
ELB improved by 0.0518774
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.711
ELB improved by 0.0506835
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.662
ELB improved by 0.0488967
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.615
ELB improved by 0.0469246
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.57
ELB improved by 0.0450921
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.527
ELB improved by 0.0436249
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.484
ELB improved by 0.0427017
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.441
ELB improved by 0.0425221
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.398
ELB improved by 0.043379
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.352
ELB improved by 0.0457665
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.302
ELB improved by 0.0505923
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.242
ELB improved by 0.0596592
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.165
ELB improved by 0.0768668
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.054
ELB improved by 0.111471
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.866
ELB improved by 0.187484
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.496
ELB improved by 0.369789
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.692
ELB improved by 0.804144
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.2
ELB improved by 1.49229
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.461
ELB improved by 1.73952
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.057
ELB improved by 1.40368
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.189
ELB improved by 0.868184
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.717
ELB improved by 0.471266
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.455
ELB improved by 0.262403
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.303
ELB improved by 0.151578
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.212
ELB improved by 0.0913384
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.153
ELB improved by 0.0589143
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.112
ELB improved by 0.0411541
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.081
ELB improved by 0.0308544
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.057
ELB improved by 0.0243902
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.037
ELB improved by 0.0199934
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.02
ELB improved by 0.0167917
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.006
ELB improved by 0.0143375
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.993
ELB improved by 0.0123876
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.982
ELB improved by 0.0108004
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.973
ELB improved by 0.00948684
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-869.52
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.391
ELB improved by 303.129
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.023
ELB improved by 60.3673
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.011
ELB improved by 35.0121
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.047
ELB improved by 14.9641
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.112
ELB improved by 6.93462
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.814
ELB improved by 5.29846
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.578
ELB improved by 5.2357
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.067
ELB improved by 5.511
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.451
ELB improved by 5.61641
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.21
ELB improved by 5.24108
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.972
ELB improved by 4.23824
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.098
ELB improved by 2.87349
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.356
ELB improved by 1.74248
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.298
ELB improved by 1.05751
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.609
ELB improved by 0.689263
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.121
ELB improved by 0.487523
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.753
ELB improved by 0.368485
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.46
ELB improved by 0.293259
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.216
ELB improved by 0.243437
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.007
ELB improved by 0.209273
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.822
ELB improved by 0.185067
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.654
ELB improved by 0.16733
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.501
ELB improved by 0.153886
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.357
ELB improved by 0.143347
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.222
ELB improved by 0.134809
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.095
ELB improved by 0.127659
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.973
ELB improved by 0.121474
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.857
ELB improved by 0.115956
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.746
ELB improved by 0.110895
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.64
ELB improved by 0.106148
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.539
ELB improved by 0.101617
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.441
ELB improved by 0.0972448
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.348
ELB improved by 0.0930017
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.26
ELB improved by 0.0888791
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.175
ELB improved by 0.0848832
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.094
ELB improved by 0.0810288
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.016
ELB improved by 0.0773345
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.942
ELB improved by 0.0738181
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.872
ELB improved by 0.0704926
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.805
ELB improved by 0.0673629
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.74
ELB improved by 0.0644236
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.679
ELB improved by 0.0616571
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.619
ELB improved by 0.0590339
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.563
ELB improved by 0.0565152
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.509
ELB improved by 0.0540576
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.457
ELB improved by 0.0516209
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.408
ELB improved by 0.0491753
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.361
ELB improved by 0.0467073
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.317
ELB improved by 0.0442207
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.275
ELB improved by 0.0417338
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.236
ELB improved by 0.0392731
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.199
ELB improved by 0.0368664
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.165
ELB improved by 0.0345385
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.132
ELB improved by 0.0323083
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.102
ELB improved by 0.0301886
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.074
ELB improved by 0.0281869
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.048
ELB improved by 0.0263064
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.023
ELB improved by 0.0245469
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407
ELB improved by 0.0229061
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.979
ELB improved by 0.02138
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.959
ELB improved by 0.0199634
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.94
ELB improved by 0.0186505
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.923
ELB improved by 0.0174351
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.907
ELB improved by 0.0163107
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.891
ELB improved by 0.015271
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.877
ELB improved by 0.0143098
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.864
ELB improved by 0.0134211
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.851
ELB improved by 0.0125992
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.839
ELB improved by 0.011839
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.828
ELB improved by 0.0111353
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.818
ELB improved by 0.0104836
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.808
ELB improved by 0.00987961
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-894.83
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-577.39
ELB improved by 317.44
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.185
ELB improved by 62.2051
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.674
ELB improved by 35.5106
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.323
ELB improved by 13.3509
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.645
ELB improved by 5.67883
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.709
ELB improved by 3.93608
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.235
ELB improved by 3.47314
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.874
ELB improved by 3.36161
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.534
ELB improved by 3.34024
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.288
ELB improved by 3.2458
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.324
ELB improved by 2.96339
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.84
ELB improved by 2.48426
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.917
ELB improved by 1.92296
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.503
ELB improved by 1.41382
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.486
ELB improved by 1.01751
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.756
ELB improved by 0.729417
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.231
ELB improved by 0.525857
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.844
ELB improved by 0.386113
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.552
ELB improved by 0.292549
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.322
ELB improved by 0.229853
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.135
ELB improved by 0.186564
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.98
ELB improved by 0.155332
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.848
ELB improved by 0.131854
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.735
ELB improved by 0.113644
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.635
ELB improved by 0.0991807
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.548
ELB improved by 0.0874625
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.47
ELB improved by 0.0777958
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.4
ELB improved by 0.06969
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.338
ELB improved by 0.0627949
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.281
ELB improved by 0.0568579
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.229
ELB improved by 0.0516942
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.182
ELB improved by 0.047166
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.139
ELB improved by 0.0431688
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.099
ELB improved by 0.039622
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.063
ELB improved by 0.0364619
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.029
ELB improved by 0.0336373
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.998
ELB improved by 0.0311064
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.969
ELB improved by 0.0288339
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.942
ELB improved by 0.0267901
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.917
ELB improved by 0.0249488
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.894
ELB improved by 0.0232874
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.872
ELB improved by 0.0217856
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.852
ELB improved by 0.0204258
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.833
ELB improved by 0.019192
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.815
ELB improved by 0.0180702
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.798
ELB improved by 0.017048
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.781
ELB improved by 0.0161144
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.766
ELB improved by 0.0152599
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.752
ELB improved by 0.014476
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.738
ELB improved by 0.0137554
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.725
ELB improved by 0.0130917
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.712
ELB improved by 0.0124791
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.7
ELB improved by 0.0119128
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.689
ELB improved by 0.0113885
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.678
ELB improved by 0.0109023
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.668
ELB improved by 0.0104509
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.658
ELB improved by 0.0100313
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.648
ELB improved by 0.00964097
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.747 0.188 2.930
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.084 | 0.004 | 0.091 | |
| getPIPs | 0.074 | 0.008 | 0.083 | |
| graper | 0.127 | 0.004 | 0.131 | |
| makeExampleData | 0.010 | 0.004 | 0.014 | |
| makeExampleDataWithUnequalGroups | 0.036 | 0.000 | 0.037 | |
| plotELBO | 0.288 | 0.000 | 0.289 | |
| plotGroupPenalties | 0.992 | 0.016 | 1.011 | |
| plotPosterior | 0.775 | 0.008 | 0.786 | |
| predict.graper | 3.096 | 0.012 | 3.119 | |
| print.graper | 0.081 | 0.000 | 0.081 | |