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This page was generated on 2024-06-19 12:10 -0400 (Wed, 19 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4687
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4402
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4351
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 739/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
frenchFISH 1.17.0  (landing page)
Adam Berman
Snapshot Date: 2024-06-18 14:00 -0400 (Tue, 18 Jun 2024)
git_url: https://git.bioconductor.org/packages/frenchFISH
git_branch: devel
git_last_commit: 5cd80d5
git_last_commit_date: 2024-04-30 11:21:00 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for frenchFISH on nebbiolo2

To the developers/maintainers of the frenchFISH package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/frenchFISH.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: frenchFISH
Version: 1.17.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:frenchFISH.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings frenchFISH_1.17.0.tar.gz
StartedAt: 2024-06-18 23:14:27 -0400 (Tue, 18 Jun 2024)
EndedAt: 2024-06-18 23:14:49 -0400 (Tue, 18 Jun 2024)
EllapsedTime: 22.0 seconds
RetCode: 0
Status:   OK  
CheckDir: frenchFISH.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:frenchFISH.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings frenchFISH_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/frenchFISH.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘frenchFISH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘frenchFISH’ version ‘1.17.0’
* 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 ‘frenchFISH’ 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 loading without being on the library search path ... 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 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

frenchFISH.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL frenchFISH
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘frenchFISH’ ...
** using staged installation
** R
** 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 (frenchFISH)

Tests output

frenchFISH.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(frenchFISH)
> 
> test_check("frenchFISH")

Number of observations  not used in the estimation process:  0
Total number of time observations:  4
Number of events:  7

Convergence code:  0
Convergence attained
Loglikelihood:  -3.083

Estimated coefficients: 
  b0 
0.56 
Full coefficients: 
  b0 
0.56 
attr(,"TypeCoeff")
[1] "Fixed: No  fixed parameters"


Number of observations  not used in the estimation process:  0
Total number of time observations:  4
Number of events:  10

Convergence code:  0
Convergence attained
Loglikelihood:  -3.884

Estimated coefficients: 
   b0 
0.223 
Full coefficients: 
   b0 
0.223 
attr(,"TypeCoeff")
[1] "Fixed: No  fixed parameters"


Number of observations  not used in the estimation process:  0
Total number of time observations:  4
Number of events:  6

Convergence code:  0
Convergence attained
Loglikelihood:  -3.863

Estimated coefficients: 
    b0 
-0.288 
Full coefficients: 
    b0 
-0.288 
attr(,"TypeCoeff")
[1] "Fixed: No  fixed parameters"


Number of observations  not used in the estimation process:  0
Total number of time observations:  2
Number of events:  1

Convergence code:  0
Convergence attained
Loglikelihood:  -1.693

Estimated coefficients: 
    b0 
-0.693 
Full coefficients: 
    b0 
-0.693 
attr(,"TypeCoeff")
[1] "Fixed: No  fixed parameters"

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
  2.314   0.125   2.429 

Example timings

frenchFISH.Rcheck/frenchFISH-Ex.timings

nameusersystemelapsed
convertFishalyserCsvToCountMatrix0.0040.0000.005
getAutomaticCountsEstimates0.1160.0080.124
getManualCountsEstimates1.2240.1001.324