Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-27 11:35:46 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 464/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crossmeta 1.28.0  (landing page)
Alex Pickering
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/crossmeta
git_branch: RELEASE_3_18
git_last_commit: 3ae7537
git_last_commit_date: 2023-10-24 10:50:52 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for crossmeta on nebbiolo2


To the developers/maintainers of the crossmeta package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/crossmeta.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: crossmeta
Version: 1.28.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings crossmeta_1.28.0.tar.gz
StartedAt: 2024-03-25 21:22:07 -0400 (Mon, 25 Mar 2024)
EndedAt: 2024-03-25 21:25:20 -0400 (Mon, 25 Mar 2024)
EllapsedTime: 192.9 seconds
RetCode: 0
Status:   OK  
CheckDir: crossmeta.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings crossmeta_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/crossmeta.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘crossmeta/DESCRIPTION’ ... OK
* this is package ‘crossmeta’ version ‘1.28.0’
* 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 ‘crossmeta’ 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 R 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘XML’
  All declared Imports should be used.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
symbol_annot 17.179  1.338  19.206
diff_expr    12.963  0.375  13.327
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘crossmeta-vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/crossmeta.Rcheck/00check.log’
for details.



Installation output

crossmeta.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL crossmeta
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘crossmeta’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (crossmeta)

Tests output

crossmeta.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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(crossmeta)
> 
> test_check("crossmeta")
GSE1_disease-healthy (# p < 0.05): 0 
GSE1_disease-healthy (# p < 0.05): 2 
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by column names.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Apoa1_ApoAI...-C57BL.6 (# p < 0.05): 20 
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
> 
> proc.time()
   user  system elapsed 
 20.204   0.505  20.699 

Example timings

crossmeta.Rcheck/crossmeta-Ex.timings

nameusersystemelapsed
add_sources0.2130.0000.213
diff_expr12.963 0.37513.327
es_meta2.1530.0602.213
filter_genes0.0490.0000.049
get_raw1.2070.0601.822
load_diff0.2220.0080.231
load_raw0.2250.0160.240
makeExampleCountsEset0.0510.0150.065
open_raw_illum0.0140.0000.014
setup_prev3.6480.2403.872
symbol_annot17.179 1.33819.206
to_ma0.0020.0040.006