Federico Marini
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: RELEASE_3_17 |
| git_last_commit: 55e4ea5 |
| git_last_commit_date: 2023-09-28 10:09:47 -0400 (Thu, 28 Sep 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:03 -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 794/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.4.2 (landing page) Federico Marini
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the GeneTonic 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: GeneTonic |
| Version: 2.4.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneTonic_2.4.2.tar.gz |
| StartedAt: 2023-10-17 21:12:15 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 21:27:57 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 942.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneTonic_2.4.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GeneTonic.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 ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.4.2’
* 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 ‘GeneTonic’ can be installed ... OK
* 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 startup messages can be suppressed ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
summarize_ggs_hubgenes 7.405 0.255 10.694
gs_mds 7.409 0.166 10.874
ggs_backbone 7.057 0.235 10.151
gs_upset 6.794 0.166 10.361
GeneTonic 6.513 0.228 10.363
ggs_graph 6.203 0.198 9.461
gs_heatmap 6.099 0.182 8.308
gs_scoresheat 5.680 0.159 8.817
signature_volcano 5.427 0.194 8.581
enhance_table 5.331 0.169 7.955
gs_dendro 5.300 0.142 8.143
gs_scores 5.181 0.160 6.739
gs_radar 4.993 0.230 7.003
gs_volcano 4.774 0.136 7.070
gene_plot 4.562 0.132 7.128
export_for_iSEE 4.522 0.134 6.464
distill_enrichment 4.343 0.136 6.524
gs_summary_overview_pair 4.346 0.133 6.423
gs_alluvial 4.181 0.184 6.303
gs_horizon 4.148 0.132 6.452
enrichment_map 4.045 0.128 5.991
get_aggrscores 4.028 0.125 6.263
GeneTonicList 3.980 0.137 5.803
checkup_GeneTonic 3.929 0.143 5.001
gs_summary_overview 3.877 0.135 5.101
gs_summary_heat 3.623 0.126 5.258
create_kappa_matrix 3.377 0.082 5.229
* 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: OK
GeneTonic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘GeneTonic’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GeneTonic)
GeneTonic.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(GeneTonic)
>
> test_check("GeneTonic")
--- Loading packages...
- Done!
--- Generating objects for the testing setup...
using counts and average transcript lengths from tximeta
'select()' returned 1:many mapping between keys and columns
estimating size factors
using 'avgTxLength' from assays(dds), correcting for library size
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
- Done!
--- Running enrichGO...
--- Running gseGO...
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
- Done!
---------------------------------
----- GeneTonicList object ------
---------------------------------
----- dds object -----
Providing an expression object (as DESeqDataset) of 17806 features over 24 samples
----- res_de object -----
Providing a DE result object (as DESeqResults), 17806 features tested, 928 found as DE
Upregulated: 599
Downregulated: 329
----- res_enrich object -----
Providing an enrichment result object, 200 reported
----- annotation_obj object -----
Providing an annotation object of 58294 features with information on 2 identifier types
--- Test setup script completed!
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[ FAIL 0 | WARN 2 | SKIP 0 | PASS 264 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 264 ]
>
> proc.time()
user system elapsed
225.282 7.796 300.009
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 6.513 | 0.228 | 10.363 | |
| GeneTonicList | 3.980 | 0.137 | 5.803 | |
| check_colors | 0.010 | 0.002 | 0.016 | |
| checkup_GeneTonic | 3.929 | 0.143 | 5.001 | |
| checkup_gtl | 3.350 | 0.131 | 4.434 | |
| cluster_markov | 0.104 | 0.005 | 0.172 | |
| create_jaccard_matrix | 0.977 | 0.061 | 1.565 | |
| create_kappa_matrix | 3.377 | 0.082 | 5.229 | |
| create_upsetdata | 0.042 | 0.041 | 0.111 | |
| deseqresult2df | 0.217 | 0.010 | 0.323 | |
| distill_enrichment | 4.343 | 0.136 | 6.524 | |
| enhance_table | 5.331 | 0.169 | 7.955 | |
| enrichment_map | 4.045 | 0.128 | 5.991 | |
| export_for_iSEE | 4.522 | 0.134 | 6.464 | |
| export_to_sif | 0.030 | 0.003 | 0.054 | |
| gene_plot | 4.562 | 0.132 | 7.128 | |
| geneinfo_2_html | 0.008 | 0.001 | 0.013 | |
| get_aggrscores | 4.028 | 0.125 | 6.263 | |
| get_expression_values | 3.109 | 0.106 | 4.853 | |
| ggs_backbone | 7.057 | 0.235 | 10.151 | |
| ggs_graph | 6.203 | 0.198 | 9.461 | |
| go_2_html | 0.023 | 0.001 | 0.036 | |
| gs_alluvial | 4.181 | 0.184 | 6.303 | |
| gs_dendro | 5.300 | 0.142 | 8.143 | |
| gs_fuzzyclustering | 1.504 | 0.056 | 2.116 | |
| gs_heatmap | 6.099 | 0.182 | 8.308 | |
| gs_horizon | 4.148 | 0.132 | 6.452 | |
| gs_mds | 7.409 | 0.166 | 10.874 | |
| gs_radar | 4.993 | 0.230 | 7.003 | |
| gs_scores | 5.181 | 0.160 | 6.739 | |
| gs_scoresheat | 5.680 | 0.159 | 8.817 | |
| gs_simplify | 1.212 | 0.038 | 1.932 | |
| gs_summary_heat | 3.623 | 0.126 | 5.258 | |
| gs_summary_overview | 3.877 | 0.135 | 5.101 | |
| gs_summary_overview_pair | 4.346 | 0.133 | 6.423 | |
| gs_upset | 6.794 | 0.166 | 10.361 | |
| gs_volcano | 4.774 | 0.136 | 7.070 | |
| happy_hour | 3.426 | 0.127 | 4.652 | |
| map2color | 0.014 | 0.003 | 0.026 | |
| overlap_coefficient | 0.001 | 0.001 | 0.000 | |
| overlap_jaccard_index | 0.000 | 0.000 | 0.001 | |
| shake_davidResult | 0.012 | 0.002 | 0.018 | |
| shake_enrichResult | 2.848 | 0.083 | 4.488 | |
| shake_enrichrResult | 0.064 | 0.003 | 0.092 | |
| shake_fgseaResult | 0.157 | 0.006 | 0.251 | |
| shake_gprofilerResult | 0.107 | 0.009 | 0.181 | |
| shake_gsenrichResult | 2.047 | 0.069 | 3.212 | |
| shake_topGOtableResult | 0.007 | 0.004 | 0.018 | |
| signature_volcano | 5.427 | 0.194 | 8.581 | |
| styleColorBar_divergent | 0.253 | 0.046 | 0.460 | |
| summarize_ggs_hubgenes | 7.405 | 0.255 | 10.694 | |