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This page was generated on 2024-11-09 21:32 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 2231/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
uSORT 1.32.0  (landing page)
Hao Chen
Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024)
git_url: https://git.bioconductor.org/packages/uSORT
git_branch: RELEASE_3_20
git_last_commit: 8111152
git_last_commit_date: 2024-10-29 10:14:04 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for uSORT on kjohnson3

To the developers/maintainers of the uSORT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/uSORT.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.

raw results


Summary

Package: uSORT
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:uSORT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings uSORT_1.32.0.tar.gz
StartedAt: 2024-11-09 16:00:42 -0500 (Sat, 09 Nov 2024)
EndedAt: 2024-11-09 16:05:27 -0500 (Sat, 09 Nov 2024)
EllapsedTime: 284.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: uSORT.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:uSORT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings uSORT_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/uSORT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘uSORT/DESCRIPTION’ ... OK
* this is package ‘uSORT’ version ‘1.32.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘uSORT’ can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/uSORT.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... NOTE
mcesApply1: no visible global function definition for ‘clusterEvalQ’
mcesApply1: no visible global function definition for ‘parRapply’
mcesApply1: no visible global function definition for ‘parCapply’
Undefined global functions or variables:
  clusterEvalQ parCapply parRapply
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
sWanderlust 7.272  1.012   8.278
autoSPIN    4.728  0.354   5.081
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/uSORT.Rcheck/00check.log’
for details.


Installation output

uSORT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL uSORT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘uSORT’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘BiocGenerics’ for request: ‘clusterEvalQ’ when loading ‘uSORT’
No methods found in package ‘BiocGenerics’ for request: ‘parCapply’ when loading ‘uSORT’
No methods found in package ‘BiocGenerics’ for request: ‘parRapply’ when loading ‘uSORT’
Note: break used in wrong context: no loop is visible 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘BiocGenerics’ for request: ‘clusterEvalQ’ when loading ‘uSORT’
No methods found in package ‘BiocGenerics’ for request: ‘parCapply’ when loading ‘uSORT’
No methods found in package ‘BiocGenerics’ for request: ‘parRapply’ when loading ‘uSORT’
** testing if installed package can be loaded from final location
No methods found in package ‘BiocGenerics’ for request: ‘clusterEvalQ’ when loading ‘uSORT’
No methods found in package ‘BiocGenerics’ for request: ‘parCapply’ when loading ‘uSORT’
No methods found in package ‘BiocGenerics’ for request: ‘parRapply’ when loading ‘uSORT’
** testing if installed package keeps a record of temporary installation path
* DONE (uSORT)

Tests output

uSORT.Rcheck/tests/runTests.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.

> BiocGenerics:::testPackage("uSORT")
No methods found in package 'BiocGenerics' for request: 'clusterEvalQ' when loading 'uSORT'
No methods found in package 'BiocGenerics' for request: 'parCapply' when loading 'uSORT'
No methods found in package 'BiocGenerics' for request: 'parRapply' when loading 'uSORT'
No starting point specified, the first row will be used!
  Building lNN graph...
    lNN computed in: 0 seconds
    Randomly Select waypoints...
    Flock waypoints...
  Iteratively realign trajectory: 
    Running iterations... 1
      Correlation with previous iteration: 0.985372
    Running iterations... 2
      Correlation with previous iteration: 0.99972
    Running iterations... 3
      Correlation with previous iteration: 0.999971
  Wanderlust Sorting Done!


RUNIT TEST PROTOCOL -- Sat Nov  9 16:05:24 2024 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
uSORT RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.853   0.359   2.211 

Example timings

uSORT.Rcheck/uSORT-Ex.timings

nameusersystemelapsed
Rwanderlust0.2480.0110.259
SPIN0.0250.0020.027
STS_sortingcost0.0060.0000.006
autoSPIN4.7280.3545.081
driving_force_gene_selection000
elbow_detection0.0020.0010.001
monocle_wrapper0.0000.0000.001
neighborhood_sortingcost0.0170.0030.020
pca_gene_selection1.0350.0481.084
sWanderlust7.2721.0128.278
uSORT000
uSORT_GUI000
uSORT_preProcess0.5490.0360.585
uSORT_sorting_wrapper0.8160.0350.851
uSORT_write_results0.0010.0010.000