Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 1529/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pirat 0.99.26  (landing page)
Samuel Wieczorek
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/Pirat
git_branch: devel
git_last_commit: 4a724fc
git_last_commit_date: 2024-06-11 05:14:08 -0400 (Tue, 11 Jun 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64  OK    ERROR  skippedskipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for Pirat on palomino6

To the developers/maintainers of the Pirat package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Pirat.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: Pirat
Version: 0.99.26
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Pirat.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Pirat_0.99.26.tar.gz
StartedAt: 2024-07-16 02:47:11 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 02:50:53 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 222.6 seconds
RetCode: 0
Status:   OK  
CheckDir: Pirat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Pirat.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Pirat_0.99.26.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/Pirat.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Pirat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pirat' version '0.99.26'
* 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 whether package 'Pirat' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/Pirat.Rcheck/00install.out' for details.
* 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
plot_pep_correlations: no visible binding for global variable 'group'
Undefined global functions or variables:
  group
* 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 line endings in shell scripts ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
rm_pg_from_idx_merge_pg 59.12   0.33   59.56
pipeline_llkimpute       6.52   0.03    6.58
impute_block_llk_reset   1.32   0.75   11.35
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test_pirat.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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/Pirat.Rcheck/00check.log'
for details.


Installation output

Pirat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Pirat
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'Pirat' ...
** using non-staged installation via StagedInstall field
** 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
* DONE (Pirat)

Tests output

Pirat.Rcheck/tests/test_pirat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> 
> proc.time()
   user  system elapsed 
   0.14    0.06    0.18 

Example timings

Pirat.Rcheck/Pirat-Ex.timings

nameusersystemelapsed
estimate_gamma0.020.000.02
estimate_psi_df0.000.020.02
get_indexes_embedded_prots000
impute_block_llk_reset 1.32 0.7511.35
impute_block_llk_reset_PG0.110.010.13
impute_from_blocks0.560.000.56
install_Pirat_env0.010.052.83
pipeline_llkimpute6.520.036.58
pirat2SE0.050.000.05
plot2hists0.010.000.01
plot_pep_correlations0.270.000.27
rm_pg_from_idx_merge_pg59.12 0.3359.56
split_large_pg000
split_large_pg_PG0.020.000.01
wrapper_pipeline_llkimpute1.370.001.38