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This page was generated on 2024-12-23 11:46 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 1975/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
smartid 1.3.2  (landing page)
Jinjin Chen
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/smartid
git_branch: devel
git_last_commit: a939065
git_last_commit_date: 2024-11-12 22:00:10 -0500 (Tue, 12 Nov 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for smartid on kjohnson3

To the developers/maintainers of the smartid package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/smartid.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: smartid
Version: 1.3.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:smartid.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings smartid_1.3.2.tar.gz
StartedAt: 2024-12-22 21:31:03 -0500 (Sun, 22 Dec 2024)
EndedAt: 2024-12-22 21:32:17 -0500 (Sun, 22 Dec 2024)
EllapsedTime: 73.9 seconds
RetCode: 0
Status:   OK  
CheckDir: smartid.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:smartid.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings smartid_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/smartid.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘smartid/DESCRIPTION’ ... OK
* this is package ‘smartid’ version ‘1.3.2’
* 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 ‘smartid’ 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 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 ... 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: OK


Installation output

smartid.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘smartid’ ...
** 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 (smartid)

Tests output

smartid.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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Type 'license()' or 'licence()' for distribution details.

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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
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Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(smartid)
> 
> test_check("smartid")
One of the variances is going to zero;  trying new starting values.
One of the variances is going to zero;  trying new starting values.
One of the variances is going to zero;  trying new starting values.
One of the variances is going to zero;  trying new starting values.
One of the variances is going to zero;  trying new starting values.
One of the variances is going to zero;  trying new starting values.
One of the variances is going to zero;  trying new starting values.
One of the variances is going to zero;  trying new starting values.
One of the variances is going to zero;  trying new starting values.
One of the variances is going to zero;  trying new starting values.
number of iterations= 15 
number of iterations= 69 
One of the variances is going to zero;  trying new starting values.
One of the variances is going to zero;  trying new starting values.
One of the variances is going to zero;  trying new starting values.
number of iterations= 39 
number of iterations= 20750 
number of iterations= 38 
number of iterations= 84 
number of iterations= 575 
number of iterations= 212 
number of iterations= 245 
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]
> 
> proc.time()
   user  system elapsed 
  7.743   0.353   8.105 

Example timings

smartid.Rcheck/smartid-Ex.timings

nameusersystemelapsed
cal_score0.0960.0040.100
cal_score_init0.0000.0010.002
gs_score000
gs_score_init000
iae000
iae_hdb0.0050.0010.006
iae_igm0.0010.0000.001
iae_m0.0000.0010.000
iae_prob000
iae_rf0.0010.0000.001
iae_sd000
idf0.0000.0010.000
idf_hdb0.0000.0000.001
idf_iae_methods0.0010.0000.000
idf_igm0.0000.0000.001
idf_m000
idf_prob0.0000.0000.001
idf_rf0.0010.0000.000
idf_sd000
markers_hdbscan0.0370.0030.040
markers_mclust0.2650.0030.270
markers_mixmdl0.2260.0180.257
ova_score_boxplot0.1530.0100.163
scale_mgm000
score_barplot0.1710.0120.184
sin_score_boxplot0.1710.0030.173
tf000
top_markers0.0250.0010.026
top_markers_abs0.0120.0000.012
top_markers_glm0.0130.0000.013
top_markers_init0.0120.0000.013