Wenjun Liu
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/sSNAPPY |
| git_branch: RELEASE_3_17 |
| git_last_commit: 4e97239 |
| git_last_commit_date: 2023-10-09 03:03:41 -0400 (Mon, 09 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:13 -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 2013/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sSNAPPY 1.4.6 (landing page) Wenjun Liu
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the sSNAPPY 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: sSNAPPY |
| Version: 1.4.6 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sSNAPPY.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sSNAPPY_1.4.6.tar.gz |
| StartedAt: 2023-10-19 04:38:22 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 04:54:30 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 967.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sSNAPPY.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sSNAPPY.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sSNAPPY_1.4.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/sSNAPPY.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 ‘sSNAPPY/DESCRIPTION’ ... OK
* this is package ‘sSNAPPY’ version ‘1.4.6’
* 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 ‘sSNAPPY’ 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 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
pathway_pert 54.713 1.884 100.315
plot_gene_contribution 49.930 2.138 94.242
raw_gene_pert 46.025 1.548 82.279
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
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
sSNAPPY.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sSNAPPY ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘sSNAPPY’ ... ** using staged installation ** 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 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 (sSNAPPY)
sSNAPPY.Rcheck/tests/spelling.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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.213 0.066 0.542
sSNAPPY.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(sSNAPPY)
Loading required package: ggplot2
>
> test_check("sSNAPPY")
Column names of the perturbation score matrix must match
the sample column of the annotation_df. Annotation df ignored.
Gene fold-changes were not provided as a named vector. All genes will be colored identically.
Gene fold-changes were not provided as a named vector. All genes will be colored identically.
Gene fold-changes were not provided as a named vector. All genes will be colored identically.
Gene fold-changes were not provided as a named vector. All genes will be colored identically.
Gene fold-changes were not provided as a named vector. All genes will be colored identically.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 104 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 104 ]
>
> proc.time()
user system elapsed
155.957 2.559 287.377
sSNAPPY.Rcheck/sSNAPPY-Ex.timings
| name | user | system | elapsed | |
| generate_permuted_scores | 0.465 | 0.013 | 0.869 | |
| normalise_by_permu | 0.000 | 0.000 | 0.001 | |
| pathway_pert | 54.713 | 1.884 | 100.315 | |
| plot_community | 1.932 | 0.076 | 3.131 | |
| plot_gene_contribution | 49.930 | 2.138 | 94.242 | |
| plot_gs2gene | 2.065 | 0.060 | 4.022 | |
| plot_gs_network | 0.648 | 0.019 | 1.191 | |
| raw_gene_pert | 46.025 | 1.548 | 82.279 | |
| retrieve_topology | 0 | 0 | 0 | |
| weight_ss_fc | 0.410 | 0.007 | 0.742 | |