| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:08 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1470/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pareg 1.4.1 (landing page) Kim Philipp Jablonski
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the pareg package: - 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: 1.4.1 |
| 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_1.4.1.tar.gz |
| StartedAt: 2023-10-18 13:34:15 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 13:40:31 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 375.7 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_1.4.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/pareg.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pareg/DESCRIPTION’ ... OK
* this is package ‘pareg’ version ‘1.4.1’
* 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-3.17-bioc-mac-arm64/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 R 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 11.761 4.064 28.793
cvedgenet-methods 9.948 0.202 15.025
edgenet-methods 3.807 0.081 5.986
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc-mac-arm64/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/4.3-arm64/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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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")
+ )
> basilisk::basiliskRun(
+ proc = cl,
+ fun = test_check,
+ "pareg"
+ )
2023-10-18 13:40:06.254607: W tensorflow/core/platform/profile_utils/cpu_utils.cc:128] Failed to get CPU frequency: 0 Hz
[ 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 0.003 0.028 0 list(mes....
2 TRUE FALSE 0 0.030 0.005 0.053 0 list(mes....
3 TRUE FALSE 0 0.004 0.000 0.006 0 list(mes....
4 TRUE FALSE 0 0.004 0.001 0.008 0 list(mes....
5 TRUE FALSE 0 0.005 0.000 0.006 0 list(mes....
6 FALSE FALSE 0 0.009 0.001 0.018 1 list(mes....
7 TRUE FALSE 0 0.005 0.000 0.007 0 list(mes....
8 TRUE FALSE 0 0.006 0.001 0.008 0 list(mes....
9 TRUE FALSE 0 0.005 0.000 0.011 0 list(mes....
10 FALSE FALSE 5 3.305 0.111 5.275 1 list(mes....
11 TRUE FALSE 0 0.004 0.000 0.005 0 list(mes....
12 TRUE FALSE 0 0.005 0.000 0.008 0 list(mes....
13 FALSE FALSE 0 0.049 0.002 0.081 1 list(mes....
14 FALSE FALSE 0 0.049 0.001 0.077 1 list(mes....
15 FALSE FALSE 0 0.250 0.023 0.416 1 list(mes....
16 FALSE FALSE 0 0.279 0.023 0.462 1 list(mes....
17 FALSE FALSE 0 0.117 0.005 0.188 2 list(mes....
18 FALSE FALSE 3 3.322 0.135 5.361 4 list(mes....
19 FALSE FALSE 0 0.012 0.002 0.023 2 list(mes....
> basilisk::basiliskStop(cl)
>
> proc.time()
user system elapsed
25.580 3.331 45.282
pareg.Rcheck/pareg-Ex.timings
| name | user | system | elapsed | |
| as.data.frame.pareg | 11.761 | 4.064 | 28.793 | |
| as_dense_sim | 0.016 | 0.001 | 0.026 | |
| as_enrichplot_object | 1.616 | 0.044 | 2.541 | |
| cluster_apply | 0.006 | 0.001 | 0.006 | |
| compute_term_similarities | 0.038 | 0.002 | 0.060 | |
| create_model_df | 0.152 | 0.007 | 0.240 | |
| cvedgenet-methods | 9.948 | 0.202 | 15.025 | |
| edgenet-methods | 3.807 | 0.081 | 5.986 | |
| family-methods | 0.023 | 0.001 | 0.039 | |
| generate_similarity_matrix | 0.032 | 0.003 | 0.052 | |
| jaccard | 0.011 | 0.001 | 0.017 | |
| overlap_coefficient | 0.019 | 0.001 | 0.033 | |
| pareg | 1.664 | 0.041 | 2.679 | |
| plot_pareg_with_args | 2.104 | 0.055 | 3.309 | |
| similarity_sample | 0.016 | 0.002 | 0.024 | |
| transform_y | 0.010 | 0.001 | 0.016 | |