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This page was generated on 2025-10-18 12:04 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 488/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CTexploreR 1.5.2  (landing page)
Axelle Loriot
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/CTexploreR
git_branch: devel
git_last_commit: 64e2ed7
git_last_commit_date: 2025-10-11 13:24:42 -0400 (Sat, 11 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK results for CTexploreR on lconway

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: 1.5.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CTexploreR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CTexploreR_1.5.2.tar.gz
StartedAt: 2025-10-17 21:18:00 -0400 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 21:30:50 -0400 (Fri, 17 Oct 2025)
EllapsedTime: 770.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CTexploreR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CTexploreR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CTexploreR_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CTexploreR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CTexploreR/DESCRIPTION’ ... OK
* this is package ‘CTexploreR’ version ‘1.5.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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                         14.178  2.214  18.722
embryos_mean_methylation              13.099  0.755  14.794
normal_tissues_methylation             9.517  0.670  10.467
normal_tissues_mean_methylation        9.242  0.647  10.366
fetal_germcells_mean_methylation       8.913  0.625  10.019
HPA_cell_type_expression               7.028  0.510   7.896
GTEX_expression                        5.621  0.545   6.749
normal_tissue_expression_multimapping  5.371  0.495   6.251
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/CTexploreR.Rcheck/00check.log’
for details.


Installation output

CTexploreR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CTexploreR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘CTexploreR’ ...
** this is package ‘CTexploreR’ version ‘1.5.2’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 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(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
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
see ?CTdata and browseVignettes('CTdata') for documentation
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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
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
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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
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see ?CTdata and browseVignettes('CTdata') for documentation
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see ?CTdata and browseVignettes('CTdata') for documentation
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see ?CTdata and browseVignettes('CTdata') for documentation
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see ?CTdata and browseVignettes('CTdata') for documentation
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see ?CTdata and browseVignettes('CTdata') for documentation
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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
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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 127 ]
Deleting unused snapshots:
• GTEX_expression/gtex-expression-on-mage.svg
> 
> proc.time()
   user  system elapsed 
300.332  35.662 422.382 

Example timings

CTexploreR.Rcheck/CTexploreR-Ex.timings

nameusersystemelapsed
CCLE_expression000
CT_correlated_genes000
CT_genes0.0670.0040.071
DAC_induction14.178 2.21418.722
GTEX_expression5.6210.5456.749
HPA_cell_type_expression7.0280.5107.896
TCGA_expression000
TCGA_methylation_expression_correlation000
all_genes0.0420.0010.043
embryo_expression000
embryos_mean_methylation13.099 0.75514.794
fetal_germcells_expression000
fetal_germcells_mean_methylation 8.913 0.62510.019
hESC_expression0.0000.0000.001
hESC_mean_methylation000
normal_tissue_expression_multimapping5.3710.4956.251
normal_tissues_mean_methylation 9.242 0.64710.366
normal_tissues_methylation 9.517 0.67010.467
oocytes_expression0.0000.0010.000
set_fontsize000
testis_expression000