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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1991/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
smartid 1.2.0  (landing page)
Jinjin Chen
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/smartid
git_branch: RELEASE_3_20
git_last_commit: 7b06ff8
git_last_commit_date: 2024-10-29 11:29:16 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for smartid on merida1

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: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2024-12-20 09:53:07 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 09:59:39 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 392.2 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/smartid.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘smartid/DESCRIPTION’ ... OK
* this is package ‘smartid’ version ‘1.2.0’
* 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/4.4-x86_64/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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.

> # 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= 20751 
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 43 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 43 ]
> 
> proc.time()
   user  system elapsed 
 59.213   1.680  62.844 

Example timings

smartid.Rcheck/smartid-Ex.timings

nameusersystemelapsed
cal_score0.3930.0330.439
cal_score_init0.0050.0070.012
gs_score0.0020.0010.003
gs_score_init0.0010.0000.001
iae0.0000.0010.002
iae_hdb0.0340.0050.040
iae_igm0.0020.0000.003
iae_m0.0020.0020.004
iae_prob0.0010.0020.005
iae_rf0.0020.0020.005
iae_sd0.0030.0010.005
idf0.0010.0010.002
idf_hdb0.0060.0020.008
idf_iae_methods0.0000.0000.001
idf_igm0.0020.0010.004
idf_m0.0010.0020.003
idf_prob0.0020.0030.005
idf_rf0.0020.0020.005
idf_sd0.0010.0010.002
markers_hdbscan0.2040.0110.216
markers_mclust0.1410.0060.150
markers_mixmdl2.1710.1622.394
ova_score_boxplot1.1560.0531.216
scale_mgm0.0020.0020.003
score_barplot1.4040.1541.572
sin_score_boxplot1.4390.0561.504
tf0.0010.0020.003
top_markers0.1190.0030.125
top_markers_abs0.0770.0010.080
top_markers_glm0.0970.0010.098
top_markers_init0.0940.0010.096