Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-27 11:36:37 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 475/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CTexploreR 0.99.5  (landing page)
Axelle Loriot
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/CTexploreR
git_branch: devel
git_last_commit: ee97824
git_last_commit_date: 2023-11-10 10:17:01 -0400 (Fri, 10 Nov 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

CHECK results for CTexploreR on nebbiolo1


To the developers/maintainers of the CTexploreR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CTexploreR.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: CTexploreR
Version: 0.99.5
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CTexploreR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CTexploreR_0.99.5.tar.gz
StartedAt: 2024-03-26 21:30:58 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 21:46:31 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 933.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CTexploreR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CTexploreR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CTexploreR_0.99.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CTexploreR.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 ‘CTexploreR/DESCRIPTION’ ... OK
* this is package ‘CTexploreR’ version ‘0.99.5’
* 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 ‘CTexploreR’ 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
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
DAC_induction                         9.394  0.779  10.639
normal_tissues_mean_methylation       8.433  1.400  10.449
normal_tissue_expression_multimapping 5.455  1.086   6.863
HPA_cell_type_expression              5.671  0.376   6.455
GTEX_expression                       5.602  0.336   6.346
* 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

CTexploreR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CTexploreR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘CTexploreR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
** 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 (CTexploreR)

Tests output

CTexploreR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
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.

> # 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(CTexploreR)
Loading required package: CTdata
> 
> test_check("CTexploreR")
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 98 ]
> 
> proc.time()
   user  system elapsed 
330.930  23.426 362.216 

Example timings

CTexploreR.Rcheck/CTexploreR-Ex.timings

nameusersystemelapsed
CCLE_expression000
CT_correlated_genes000
CT_genes0.0510.0160.067
DAC_induction 9.394 0.77910.639
GTEX_expression5.6020.3366.346
HPA_cell_type_expression5.6710.3766.455
TCGA_expression000
TCGA_methylation_expression_correlation000
check_names0.0000.0010.000
normal_tissue_expression_multimapping5.4551.0866.863
normal_tissues_mean_methylation 8.433 1.40010.449
normal_tissues_methylation2.5880.3963.139
prepare_TCGA_methylation_expression0.0010.0000.000
set_fontsize000
subset_database1.2910.0961.470
testis_expression000