Britta Velten
| Snapshot Date: 2025-11-17 13:45 -0500 (Mon, 17 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_22 |
| git_last_commit: 76fc31b |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-20 12:03 -0500 (Thu, 20 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 922/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.26.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graper_1.26.0.tar.gz |
| StartedAt: 2025-11-18 04:47:53 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 04:49:25 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graper_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.26.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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=-825.193
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.121
ELB improved by 258.072
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-502.933
ELB improved by 64.1886
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.304
ELB improved by 39.6286
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.617
ELB improved by 16.687
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.039
ELB improved by 7.57808
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.001
ELB improved by 5.03791
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.422
ELB improved by 4.57904
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.838
ELB improved by 4.58399
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.215
ELB improved by 4.62303
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.689
ELB improved by 4.52591
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.468
ELB improved by 4.2209
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.715
ELB improved by 3.75336
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.538
ELB improved by 3.1773
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.065
ELB improved by 2.47231
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.287
ELB improved by 1.778
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.013
ELB improved by 1.27379
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.067
ELB improved by 0.946868
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.34
ELB improved by 0.726793
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.766
ELB improved by 0.573896
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.298
ELB improved by 0.467957
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.905
ELB improved by 0.393315
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.566
ELB improved by 0.338553
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.269
ELB improved by 0.296972
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.004
ELB improved by 0.265161
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.762
ELB improved by 0.241485
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.537
ELB improved by 0.225152
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.322
ELB improved by 0.215681
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.109
ELB improved by 0.212332
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.896
ELB improved by 0.213171
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.682
ELB improved by 0.214034
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.473
ELB improved by 0.208884
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.28
ELB improved by 0.193466
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.11
ELB improved by 0.169813
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.965
ELB improved by 0.144532
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.843
ELB improved by 0.122368
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.739
ELB improved by 0.104117
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.65
ELB improved by 0.0889511
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.574
ELB improved by 0.0762168
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.508
ELB improved by 0.0656379
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.451
ELB improved by 0.0570111
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.401
ELB improved by 0.0500507
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.357
ELB improved by 0.0444166
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.317
ELB improved by 0.0397888
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.281
ELB improved by 0.035911
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.248
ELB improved by 0.0325969
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.219
ELB improved by 0.0297171
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.191
ELB improved by 0.027183
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.166
ELB improved by 0.0249325
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.144
ELB improved by 0.0229207
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.122
ELB improved by 0.0211136
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.103
ELB improved by 0.0194845
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.085
ELB improved by 0.0180117
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.068
ELB improved by 0.0166771
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.053
ELB improved by 0.0154652
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.038
ELB improved by 0.0143628
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.025
ELB improved by 0.0133584
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.013
ELB improved by 0.0124418
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.001
ELB improved by 0.0116041
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.99
ELB improved by 0.0108376
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.98
ELB improved by 0.0101351
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.971
ELB improved by 0.0094907
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-889.46
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-582.224
ELB improved by 307.236
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.087
ELB improved by 59.137
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.56
ELB improved by 39.527
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.034
ELB improved by 21.5257
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.173
ELB improved by 9.86128
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.196
ELB improved by 4.97697
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.681
ELB improved by 3.51467
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.703
ELB improved by 2.97824
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.955
ELB improved by 2.74811
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.333
ELB improved by 2.62258
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.821
ELB improved by 2.51177
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.456
ELB improved by 2.36435
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.309
ELB improved by 2.14736
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.455
ELB improved by 1.85394
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.944
ELB improved by 1.51132
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.775
ELB improved by 1.16916
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.901
ELB improved by 0.873578
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.254
ELB improved by 0.647479
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.765
ELB improved by 0.488747
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.383
ELB improved by 0.381873
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.073
ELB improved by 0.309947
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.813
ELB improved by 0.260214
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.588
ELB improved by 0.224579
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.39
ELB improved by 0.198291
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.211
ELB improved by 0.178566
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.048
ELB improved by 0.163672
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.895
ELB improved by 0.152428
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.751
ELB improved by 0.143979
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.614
ELB improved by 0.13769
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.481
ELB improved by 0.133092
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.351
ELB improved by 0.12984
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.223
ELB improved by 0.127682
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.097
ELB improved by 0.126442
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.971
ELB improved by 0.125999
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.844
ELB improved by 0.126289
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.717
ELB improved by 0.127298
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.588
ELB improved by 0.129086
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.456
ELB improved by 0.131806
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.32
ELB improved by 0.135757
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.179
ELB improved by 0.141462
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.029
ELB improved by 0.149805
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.867
ELB improved by 0.162214
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.686
ELB improved by 0.180819
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.478
ELB improved by 0.208167
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.232
ELB improved by 0.245463
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.943
ELB improved by 0.288913
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.614
ELB improved by 0.32898
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.255
ELB improved by 0.359109
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.872
ELB improved by 0.383269
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.462
ELB improved by 0.410475
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.014
ELB improved by 0.447161
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.523
ELB improved by 0.491952
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.991
ELB improved by 0.531497
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.44
ELB improved by 0.551038
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.887
ELB improved by 0.553036
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.338
ELB improved by 0.548933
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.796
ELB improved by 0.541613
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.271
ELB improved by 0.525863
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.77
ELB improved by 0.500333
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.297
ELB improved by 0.473539
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.841
ELB improved by 0.455645
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.393
ELB improved by 0.448069
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.953
ELB improved by 0.440152
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.537
ELB improved by 0.416236
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.166
ELB improved by 0.370099
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.856
ELB improved by 0.310233
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.606
ELB improved by 0.250036
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.408
ELB improved by 0.198156
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.251
ELB improved by 0.157166
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.125
ELB improved by 0.126156
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.022
ELB improved by 0.103048
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.936
ELB improved by 0.0857646
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.863
ELB improved by 0.0726341
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.801
ELB improved by 0.0624368
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.747
ELB improved by 0.0543287
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.699
ELB improved by 0.0477423
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.656
ELB improved by 0.0423007
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.619
ELB improved by 0.0377562
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.585
ELB improved by 0.0339476
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.554
ELB improved by 0.0307739
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.526
ELB improved by 0.0281788
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.5
ELB improved by 0.026145
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.475
ELB improved by 0.024698
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.451
ELB improved by 0.0239228
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.427
ELB improved by 0.0240022
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.402
ELB improved by 0.0252913
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.373
ELB improved by 0.0284592
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.339
ELB improved by 0.0347186
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.293
ELB improved by 0.0460352
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.228
ELB improved by 0.0645534
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.139
ELB improved by 0.0890367
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.031
ELB improved by 0.108398
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.924
ELB improved by 0.107038
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.837
ELB improved by 0.0869791
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.772
ELB improved by 0.0647082
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.723
ELB improved by 0.0490869
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.683
ELB improved by 0.0398196
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.649
ELB improved by 0.0343734
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.618
ELB improved by 0.0307452
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.59
ELB improved by 0.0277354
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.565
ELB improved by 0.0247588
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.544
ELB improved by 0.021657
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.525
ELB improved by 0.0185259
iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.51
ELB improved by 0.0155551
iteration 106
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.497
ELB improved by 0.0129106
iteration 107
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.486
ELB improved by 0.0106818
iteration 108
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.477
ELB improved by 0.00888191
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-866.585
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.622
ELB improved by 294.963
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.595
ELB improved by 63.027
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.613
ELB improved by 40.9813
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.748
ELB improved by 15.865
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.416
ELB improved by 6.33203
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.042
ELB improved by 4.37389
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.149
ELB improved by 3.89293
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.366
ELB improved by 3.78336
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.544
ELB improved by 3.82171
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.612
ELB improved by 3.93269
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.558
ELB improved by 4.05363
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.486
ELB improved by 4.07245
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.651
ELB improved by 3.83422
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.394
ELB improved by 3.25708
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.923
ELB improved by 2.47107
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.179
ELB improved by 1.74405
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.94
ELB improved by 1.23959
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.991
ELB improved by 0.948686
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.195
ELB improved by 0.796392
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.475
ELB improved by 0.719908
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.793
ELB improved by 0.682056
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.129
ELB improved by 0.66349
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.474
ELB improved by 0.65495
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.821
ELB improved by 0.65264
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.166
ELB improved by 0.655705
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.501
ELB improved by 0.664815
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.82
ELB improved by 0.681383
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.112
ELB improved by 0.707138
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.369
ELB improved by 0.743638
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.578
ELB improved by 0.79049
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.738
ELB improved by 0.840145
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.866
ELB improved by 0.872581
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.998
ELB improved by 0.867408
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.171
ELB improved by 0.827571
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.401
ELB improved by 0.769836
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.698
ELB improved by 0.702454
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.072
ELB improved by 0.626538
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.527
ELB improved by 0.544498
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.066
ELB improved by 0.461035
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.685
ELB improved by 0.381072
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.376
ELB improved by 0.309529
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.125
ELB improved by 0.25034
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.92
ELB improved by 0.204916
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.748
ELB improved by 0.172371
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.597
ELB improved by 0.150649
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.46
ELB improved by 0.137508
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.328
ELB improved by 0.131564
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.196
ELB improved by 0.132696
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.055
ELB improved by 0.140178
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.907
ELB improved by 0.148872
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.758
ELB improved by 0.148153
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.628
ELB improved by 0.130449
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.526
ELB improved by 0.102097
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.45
ELB improved by 0.076204
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.391
ELB improved by 0.0583335
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.344
ELB improved by 0.0468544
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.305
ELB improved by 0.0390606
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.272
ELB improved by 0.0332985
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.243
ELB improved by 0.0287545
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.218
ELB improved by 0.0250307
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.196
ELB improved by 0.021913
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.177
ELB improved by 0.0192701
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.16
ELB improved by 0.0170118
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.145
ELB improved by 0.0150711
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.132
ELB improved by 0.0133957
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.12
ELB improved by 0.0119435
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.109
ELB improved by 0.0106806
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.099
ELB improved by 0.00957855
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-843.472
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-600.871
ELB improved by 242.601
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-539.203
ELB improved by 61.6676
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.13
ELB improved by 49.073
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.003
ELB improved by 30.127
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.837
ELB improved by 15.1664
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.241
ELB improved by 7.59576
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.161
ELB improved by 5.08063
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.482
ELB improved by 4.67882
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.328
ELB improved by 5.15428
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.352
ELB improved by 5.97569
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.818
ELB improved by 6.53377
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.734
ELB improved by 6.08445
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.071
ELB improved by 4.66234
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.93
ELB improved by 3.14115
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.85
ELB improved by 2.08062
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.369
ELB improved by 1.48075
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.196
ELB improved by 1.17277
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.171
ELB improved by 1.02469
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.21
ELB improved by 0.960992
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.268
ELB improved by 0.942012
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.321
ELB improved by 0.947284
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.355
ELB improved by 0.966135
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.362
ELB improved by 0.99288
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.338
ELB improved by 1.0243
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.28
ELB improved by 1.05793
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.19
ELB improved by 1.09011
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.076
ELB improved by 1.11382
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.959
ELB improved by 1.11697
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.875
ELB improved by 1.08349
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.875
ELB improved by 1.0002
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.007
ELB improved by 0.868265
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.299
ELB improved by 0.708318
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.748
ELB improved by 0.550147
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.332
ELB improved by 0.416195
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.018
ELB improved by 0.314306
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.777
ELB improved by 0.24131
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.587
ELB improved by 0.189325
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.437
ELB improved by 0.150071
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.32
ELB improved by 0.117622
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.23
ELB improved by 0.0899195
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.162
ELB improved by 0.0675872
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.111
ELB improved by 0.051157
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.071
ELB improved by 0.0398458
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.039
ELB improved by 0.0321966
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.012
ELB improved by 0.0268978
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.989
ELB improved by 0.0230561
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.969
ELB improved by 0.0201335
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.951
ELB improved by 0.0178174
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.935
ELB improved by 0.0159237
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.921
ELB improved by 0.0143388
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.908
ELB improved by 0.012989
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.896
ELB improved by 0.0118241
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.885
ELB improved by 0.0108083
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.875
ELB improved by 0.00991528
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.433 0.172 2.592
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.051 | 0.003 | 0.053 | |
| getPIPs | 0.049 | 0.002 | 0.052 | |
| graper | 0.080 | 0.005 | 0.084 | |
| makeExampleData | 0.010 | 0.001 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.012 | 0.001 | 0.012 | |
| plotELBO | 0.328 | 0.017 | 0.345 | |
| plotGroupPenalties | 1.150 | 0.053 | 1.203 | |
| plotPosterior | 0.713 | 0.010 | 0.723 | |
| predict.graper | 2.075 | 0.017 | 2.092 | |
| print.graper | 0.049 | 0.003 | 0.051 | |