Britta Velten
| Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 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 2025-09-01 11:41 -0400 (Mon, 01 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" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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. |
| Package: graper |
| Version: 1.24.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.24.2.tar.gz |
| StartedAt: 2025-08-29 23:24:03 -0400 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 23:25:13 -0400 (Fri, 29 Aug 2025) |
| EllapsedTime: 70.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.24.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* 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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* 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 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
‘/Users/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.24.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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=-859.278
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.716
ELB improved by 285.563
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.669
ELB improved by 56.0465
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.549
ELB improved by 32.12
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.312
ELB improved by 15.2373
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.86
ELB improved by 8.4522
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.11
ELB improved by 6.74994
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.637
ELB improved by 6.47269
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.811
ELB improved by 5.82633
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.396
ELB improved by 4.41503
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.545
ELB improved by 2.85098
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.774
ELB improved by 1.7705
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.561
ELB improved by 1.21351
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.59
ELB improved by 0.970499
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.7
ELB improved by 0.889933
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.818
ELB improved by 0.882544
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.929
ELB improved by 0.88907
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.043
ELB improved by 0.885635
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.178
ELB improved by 0.864951
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.348
ELB improved by 0.830151
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.554
ELB improved by 0.794089
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.791
ELB improved by 0.763042
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.053
ELB improved by 0.738364
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.329
ELB improved by 0.723166
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.605
ELB improved by 0.723942
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.857
ELB improved by 0.748266
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.062
ELB improved by 0.794709
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.211
ELB improved by 0.851357
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.266
ELB improved by 0.945597
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.175
ELB improved by 1.09044
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.072
ELB improved by 1.10314
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.096
ELB improved by 0.976234
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.23
ELB improved by 0.866088
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.402
ELB improved by 0.827512
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.517
ELB improved by 0.885045
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.585
ELB improved by 0.932489
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.782
ELB improved by 0.802142
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.161
ELB improved by 0.621213
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.676
ELB improved by 0.485368
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.288
ELB improved by 0.387914
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.971
ELB improved by 0.316697
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.708
ELB improved by 0.263114
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.488
ELB improved by 0.22049
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.303
ELB improved by 0.184463
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.15
ELB improved by 0.153172
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.023
ELB improved by 0.126531
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.919
ELB improved by 0.10494
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.83
ELB improved by 0.0883827
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.754
ELB improved by 0.0763362
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.686
ELB improved by 0.0681023
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.623
ELB improved by 0.0631312
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.561
ELB improved by 0.0611726
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.499
ELB improved by 0.0622274
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.433
ELB improved by 0.0661833
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.361
ELB improved by 0.0719095
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.285
ELB improved by 0.0761396
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.211
ELB improved by 0.0743041
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.146
ELB improved by 0.0649404
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.094
ELB improved by 0.0521308
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.053
ELB improved by 0.0410033
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.019
ELB improved by 0.0334713
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.99
ELB improved by 0.0289817
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.964
ELB improved by 0.0264948
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.938
ELB improved by 0.0252844
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.913
ELB improved by 0.0249602
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.888
ELB improved by 0.0253151
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.862
ELB improved by 0.0261855
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.835
ELB improved by 0.0273299
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.806
ELB improved by 0.0283273
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.778
ELB improved by 0.0285609
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.75
ELB improved by 0.0274106
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.726
ELB improved by 0.0246523
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.705
ELB improved by 0.0207348
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.688
ELB improved by 0.0165542
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.675
ELB improved by 0.0128968
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.665
ELB improved by 0.0101014
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.657
ELB improved by 0.0081258
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-826.031
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-554.211
ELB improved by 271.821
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-496.501
ELB improved by 57.7099
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.105
ELB improved by 36.3952
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.208
ELB improved by 17.8971
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.86
ELB improved by 8.34863
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.949
ELB improved by 4.91047
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.81
ELB improved by 4.13879
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.644
ELB improved by 4.16623
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.266
ELB improved by 4.37835
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.854
ELB improved by 4.41214
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.846
ELB improved by 4.00754
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.604
ELB improved by 3.24207
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.13
ELB improved by 2.47411
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.184
ELB improved by 1.94582
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.524
ELB improved by 1.6604
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.997
ELB improved by 1.52654
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.539
ELB improved by 1.45775
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.141
ELB improved by 1.39896
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.813
ELB improved by 1.32729
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.571
ELB improved by 1.24228
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.418
ELB improved by 1.15268
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.351
ELB improved by 1.067
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.361
ELB improved by 0.990356
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.436
ELB improved by 0.925296
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.562
ELB improved by 0.873507
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.725
ELB improved by 0.837543
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.901
ELB improved by 0.82355
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.051
ELB improved by 0.84969
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.072
ELB improved by 0.978903
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.652
ELB improved by 1.42064
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.395
ELB improved by 2.25719
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.841
ELB improved by 2.55346
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.458
ELB improved by 2.38298
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.378
ELB improved by 2.08021
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.708
ELB improved by 1.66968
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.457
ELB improved by 1.25101
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.533
ELB improved by 0.924181
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.828
ELB improved by 0.704887
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.244
ELB improved by 0.584427
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.724
ELB improved by 0.519469
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.325
ELB improved by 0.398965
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.082
ELB improved by 0.243576
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.937
ELB improved by 0.144683
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.839
ELB improved by 0.0978521
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.762
ELB improved by 0.0773575
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.691
ELB improved by 0.0704109
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.62
ELB improved by 0.0719377
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.541
ELB improved by 0.0786669
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.456
ELB improved by 0.0848576
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.374
ELB improved by 0.0818778
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.308
ELB improved by 0.0663455
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.262
ELB improved by 0.0459722
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.232
ELB improved by 0.0299136
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.212
ELB improved by 0.0203129
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.196
ELB improved by 0.0151254
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.184
ELB improved by 0.0122108
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.174
ELB improved by 0.0103667
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.165
ELB improved by 0.00904596
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-846.551
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-560.454
ELB improved by 286.097
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.063
ELB improved by 56.3911
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.482
ELB improved by 34.5809
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.994
ELB improved by 15.4882
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.563
ELB improved by 6.43164
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.277
ELB improved by 3.28546
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.021
ELB improved by 2.25599
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.143
ELB improved by 1.87795
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.427
ELB improved by 1.71626
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.783
ELB improved by 1.64375
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.174
ELB improved by 1.60948
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.584
ELB improved by 1.59004
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.011
ELB improved by 1.57277
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.463
ELB improved by 1.54794
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.958
ELB improved by 1.50484
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.527
ELB improved by 1.43065
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.214
ELB improved by 1.31378
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.062
ELB improved by 1.15207
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.103
ELB improved by 0.959037
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.342
ELB improved by 0.760336
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.76
ELB improved by 0.582051
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.321
ELB improved by 0.439616
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.985
ELB improved by 0.335029
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.724
ELB improved by 0.261817
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.512
ELB improved by 0.211245
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.337
ELB improved by 0.175811
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.186
ELB improved by 0.150173
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.056
ELB improved by 0.130862
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.94
ELB improved by 0.115721
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.836
ELB improved by 0.103423
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.743
ELB improved by 0.0931446
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.659
ELB improved by 0.0843657
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.582
ELB improved by 0.0767459
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.512
ELB improved by 0.0700547
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.448
ELB improved by 0.0641291
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.389
ELB improved by 0.058849
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.335
ELB improved by 0.0541223
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.285
ELB improved by 0.0498758
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.239
ELB improved by 0.0460496
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.196
ELB improved by 0.0425933
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.157
ELB improved by 0.0394642
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.12
ELB improved by 0.0366255
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.086
ELB improved by 0.0340451
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.055
ELB improved by 0.031695
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.025
ELB improved by 0.0295508
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.998
ELB improved by 0.0275909
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.972
ELB improved by 0.0257964
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.948
ELB improved by 0.0241505
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.925
ELB improved by 0.0226385
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.904
ELB improved by 0.0212474
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.884
ELB improved by 0.0199656
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.865
ELB improved by 0.0187828
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.847
ELB improved by 0.01769
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.831
ELB improved by 0.016679
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.815
ELB improved by 0.0157425
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.8
ELB improved by 0.014874
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.786
ELB improved by 0.0140678
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.773
ELB improved by 0.0133185
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.76
ELB improved by 0.0126215
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.748
ELB improved by 0.0119724
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.737
ELB improved by 0.0113674
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.726
ELB improved by 0.010803
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.716
ELB improved by 0.010276
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.706
ELB improved by 0.00978342
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.734
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-597.021
ELB improved by 259.713
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-537.441
ELB improved by 59.5804
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.426
ELB improved by 47.0151
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.912
ELB improved by 24.5138
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.788
ELB improved by 10.1243
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.788
ELB improved by 4.9996
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.994
ELB improved by 3.79442
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.416
ELB improved by 3.57732
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.845
ELB improved by 3.57172
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.236
ELB improved by 3.60833
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.611
ELB improved by 3.62491
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.058
ELB improved by 3.55313
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.797
ELB improved by 3.26166
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.104
ELB improved by 2.69239
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.11
ELB improved by 1.99435
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.749
ELB improved by 1.36054
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.853
ELB improved by 0.896041
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.25
ELB improved by 0.60272
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.82
ELB improved by 0.430329
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.491
ELB improved by 0.328743
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.226
ELB improved by 0.265549
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.003
ELB improved by 0.223329
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.809
ELB improved by 0.193251
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.639
ELB improved by 0.170758
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.485
ELB improved by 0.153368
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.346
ELB improved by 0.139631
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.217
ELB improved by 0.128644
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.097
ELB improved by 0.11981
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.984
ELB improved by 0.112713
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.877
ELB improved by 0.107052
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.775
ELB improved by 0.102602
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.675
ELB improved by 0.0991895
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.579
ELB improved by 0.0966816
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.484
ELB improved by 0.0949721
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.39
ELB improved by 0.0939766
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.296
ELB improved by 0.0936273
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.202
ELB improved by 0.0938695
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.108
ELB improved by 0.0946591
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.012
ELB improved by 0.0959608
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.914
ELB improved by 0.0977476
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.814
ELB improved by 0.0999998
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.711
ELB improved by 0.102705
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.605
ELB improved by 0.105861
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.496
ELB improved by 0.10947
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.382
ELB improved by 0.11355
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.264
ELB improved by 0.118125
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.141
ELB improved by 0.123229
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.012
ELB improved by 0.128906
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.877
ELB improved by 0.135203
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.735
ELB improved by 0.142165
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.585
ELB improved by 0.149826
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.427
ELB improved by 0.158198
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.26
ELB improved by 0.167257
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.083
ELB improved by 0.176933
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.895
ELB improved by 0.187116
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.698
ELB improved by 0.197673
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.489
ELB improved by 0.208521
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.269
ELB improved by 0.219784
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.037
ELB improved by 0.232129
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.79
ELB improved by 0.247468
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.52
ELB improved by 0.270208
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.211
ELB improved by 0.308193
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.845
ELB improved by 0.366713
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.42
ELB improved by 0.424419
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.988
ELB improved by 0.432101
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.604
ELB improved by 0.384476
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.286
ELB improved by 0.317771
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.035
ELB improved by 0.250619
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.847
ELB improved by 0.188761
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.709
ELB improved by 0.137452
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.61
ELB improved by 0.0989694
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.538
ELB improved by 0.0718766
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.485
ELB improved by 0.0533375
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.444
ELB improved by 0.0407137
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.412
ELB improved by 0.0320355
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.386
ELB improved by 0.0259613
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.365
ELB improved by 0.0216114
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.346
ELB improved by 0.0184157
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.33
ELB improved by 0.0160045
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.316
ELB improved by 0.0141361
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.303
ELB improved by 0.0126511
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.292
ELB improved by 0.0114429
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.282
ELB improved by 0.0104392
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.272
ELB improved by 0.00959027
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.674 0.212 2.892
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.085 | 0.016 | 0.102 | |
| getPIPs | 0.080 | 0.012 | 0.094 | |
| graper | 0.132 | 0.016 | 0.149 | |
| makeExampleData | 0.011 | 0.001 | 0.013 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.002 | 0.015 | |
| plotELBO | 0.241 | 0.016 | 0.257 | |
| plotGroupPenalties | 0.764 | 0.017 | 0.784 | |
| plotPosterior | 0.572 | 0.019 | 0.615 | |
| predict.graper | 2.086 | 0.068 | 2.181 | |
| print.graper | 0.081 | 0.011 | 0.094 | |