Kim Philipp Jablonski
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/pareg |
| git_branch: devel |
| git_last_commit: 3581c30 |
| git_last_commit_date: 2023-10-24 11:41:09 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:39:44 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1494/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pareg 1.7.0 (landing page) Kim Philipp Jablonski
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the pareg package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pareg.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: pareg |
| Version: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pareg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pareg_1.7.0.tar.gz |
| StartedAt: 2024-03-27 23:03:28 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 23:08:50 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 322.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pareg.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pareg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pareg_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/pareg.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pareg/DESCRIPTION’ ... OK
* this is package ‘pareg’ version ‘1.7.0’
* 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 ... NOTE
Found the following non-portable file paths:
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/config.yaml
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/params.csv
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/config.yaml
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/params.csv
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/config.yaml
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/params.csv
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/config.yaml
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/params.csv
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter/config.yaml
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter/params.csv
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_response_distribution/config.yaml
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_response_distribution/params.csv
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/config.yaml
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/params.csv
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/workflow/scripts/compare_rocauc_vs_loss.R
pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pareg’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/pareg.Rcheck/00install.out’ for details.
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
as.data.frame.pareg 11.069 3.329 35.011
cvedgenet-methods 9.729 0.220 10.045
* 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-3.19-bioc/meat/pareg.Rcheck/00check.log’
for details.
pareg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pareg ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘pareg’ ... ** using non-staged installation via StagedInstall field ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (pareg)
pareg.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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(pareg)
Loading required package: tensorflow
Loading required package: tfprobability
Attaching package: 'pareg'
The following objects are masked from 'package:stats':
family, gaussian
The following object is masked from 'package:base':
beta
>
> cl <- basilisk::basiliskStart(
+ pareg::pareg_env,
+ testload = c("tensorflow", "tensorflow_probability")
+ )
2024-03-27 23:08:27.342103: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
> basilisk::basiliskRun(
+ proc = cl,
+ fun = test_check,
+ "pareg"
+ )
2024-03-27 23:08:34.459771: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
[ FAIL 0 | WARN 8 | SKIP 10 | PASS 14 ]
══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On Bioconductor (10): 'test-netreg.R:2:3', 'test-netreg.R:19:3',
'test-netreg.R:48:3', 'test-netreg.R:76:3', 'test-netreg.R:108:3',
'test-pareg.R:2:3', 'test-pareg.R:38:3', 'test-pareg.R:82:3',
'test-pareg.R:146:3', 'test-pareg.R:196:3'
[ FAIL 0 | WARN 8 | SKIP 10 | PASS 14 ]
file context
1 test-netreg.R
2 test-netreg.R
3 test-netreg.R
4 test-netreg.R
5 test-netreg.R
6 test-netreg.R
7 test-pareg.R
8 test-pareg.R
9 test-pareg.R
10 test-pareg.R
11 test-pareg.R
12 test-pareg.R
13 test-term_similarities.R
14 test-term_similarities.R
15 test-utils.R
16 test-utils.R
17 test-utils.R
18 test-utils.R
19 test-utils.R
test nb failed
1 Gaussian case works 1 0
2 Beta case works 1 0
3 Cross-validation works 1 0
4 Cross-validation with network regularization works 1 0
5 Cross-validation with network regularization works in parallel 1 0
6 laplacian computation works 1 0
7 package doesn't crash for trivial case 1 0
8 pareg works with term network 1 0
9 Bernoulli family works 1 0
10 term input network mismatch leads to crash 6 0
11 sequential cross-validation works 1 0
12 parallelized cross-validation works 1 0
13 term similarities can be computed 1 0
14 term similarities can be computed on tibble 1 0
15 model creation works with only common genes 1 0
16 model creation works with gene which is in no term 1 0
17 similarity sampling works 2 0
18 enrichplot integration works 7 0
19 tensorflow integration works 2 0
skipped error warning user system real passed result
1 TRUE FALSE 0 0.015 0.004 0.020 0 list(mes....
2 TRUE FALSE 0 0.029 0.002 0.031 0 list(mes....
3 TRUE FALSE 0 0.004 0.001 0.005 0 list(mes....
4 TRUE FALSE 0 0.004 0.001 0.006 0 list(mes....
5 TRUE FALSE 0 0.005 0.001 0.006 0 list(mes....
6 FALSE FALSE 0 0.010 0.001 0.012 1 list(mes....
7 TRUE FALSE 0 0.004 0.001 0.006 0 list(mes....
8 TRUE FALSE 0 0.005 0.002 0.006 0 list(mes....
9 TRUE FALSE 0 0.005 0.001 0.005 0 list(mes....
10 FALSE FALSE 5 2.992 0.129 3.143 1 list(mes....
11 TRUE FALSE 0 0.004 0.001 0.006 0 list(mes....
12 TRUE FALSE 0 0.004 0.001 0.005 0 list(mes....
13 FALSE FALSE 0 0.036 0.002 0.039 1 list(mes....
14 FALSE FALSE 0 0.030 0.002 0.032 1 list(mes....
15 FALSE FALSE 0 0.156 0.004 0.160 1 list(mes....
16 FALSE FALSE 0 0.126 0.002 0.130 1 list(mes....
17 FALSE FALSE 0 0.118 0.007 0.126 2 list(mes....
18 FALSE FALSE 3 2.517 0.112 2.648 4 list(mes....
19 FALSE FALSE 0 0.014 0.003 0.017 2 list(mes....
> basilisk::basiliskStop(cl)
>
> proc.time()
user system elapsed
23.827 3.457 27.440
pareg.Rcheck/pareg-Ex.timings
| name | user | system | elapsed | |
| as.data.frame.pareg | 11.069 | 3.329 | 35.011 | |
| as_dense_sim | 0.000 | 0.000 | 0.001 | |
| as_enrichplot_object | 1.631 | 0.046 | 1.684 | |
| cluster_apply | 0.000 | 0.001 | 0.000 | |
| compute_term_similarities | 0.010 | 0.001 | 0.010 | |
| create_model_df | 0.095 | 0.003 | 0.099 | |
| cvedgenet-methods | 9.729 | 0.220 | 10.045 | |
| edgenet-methods | 3.855 | 0.083 | 3.981 | |
| family-methods | 0.001 | 0.001 | 0.002 | |
| generate_similarity_matrix | 0.008 | 0.000 | 0.009 | |
| jaccard | 0 | 0 | 0 | |
| overlap_coefficient | 0 | 0 | 0 | |
| pareg | 1.534 | 0.044 | 1.582 | |
| plot_pareg_with_args | 2.160 | 0.058 | 2.222 | |
| similarity_sample | 0.005 | 0.002 | 0.008 | |
| transform_y | 0 | 0 | 0 | |