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This page was generated on 2024-04-18 11:32:20 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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 2050/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sSNAPPY 1.6.2  (landing page)
Wenjun Liu
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/sSNAPPY
git_branch: RELEASE_3_18
git_last_commit: 3e9f3c0
git_last_commit_date: 2024-04-02 09:01:52 -0400 (Tue, 02 Apr 2024)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for sSNAPPY on kjohnson1


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.

raw results


Summary

Package: sSNAPPY
Version: 1.6.2
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_1.6.2.tar.gz
StartedAt: 2024-04-18 05:21:53 -0400 (Thu, 18 Apr 2024)
EndedAt: 2024-04-18 05:32:53 -0400 (Thu, 18 Apr 2024)
EllapsedTime: 660.1 seconds
RetCode: 0
Status:   OK  
CheckDir: sSNAPPY.Rcheck
Warnings: 0

Command output

##############################################################################
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### 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_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/sSNAPPY.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sSNAPPY/DESCRIPTION’ ... OK
* this is package ‘sSNAPPY’ version ‘1.6.2’
* 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 ‘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           68.358  1.948  72.910
plot_gene_contribution 59.974  1.932  63.429
raw_gene_pert          56.039  1.420  59.234
* 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


Installation output

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)

Tests output

sSNAPPY.Rcheck/tests/spelling.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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 
  0.232   0.065   0.287 

sSNAPPY.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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 18 | SKIP 0 | PASS 103 ]

[ FAIL 0 | WARN 18 | SKIP 0 | PASS 103 ]
> 
> proc.time()
   user  system elapsed 
100.743   2.206 110.766 

Example timings

sSNAPPY.Rcheck/sSNAPPY-Ex.timings

nameusersystemelapsed
generate_permuted_scores1.2470.0171.290
normalise_by_permu0.0000.0000.001
pathway_pert68.358 1.94872.910
plot_community2.0700.0952.315
plot_gene_contribution59.974 1.93263.429
plot_gs2gene2.0960.0842.244
plot_gs_network0.8000.0120.825
raw_gene_pert56.039 1.42059.234
retrieve_topology0.0010.0000.001
weight_ss_fc0.3730.0050.378