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This page was generated on 2025-10-02 11:38 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4831
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4612
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4584
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 1062/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IntEREst 1.32.0  (landing page)
Ali Oghabian
Snapshot Date: 2025-09-29 13:40 -0400 (Mon, 29 Sep 2025)
git_url: https://git.bioconductor.org/packages/IntEREst
git_branch: RELEASE_3_21
git_last_commit: c32f5ba
git_last_commit_date: 2025-04-15 11:09:17 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for IntEREst on nebbiolo1

To the developers/maintainers of the IntEREst package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IntEREst.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: IntEREst
Version: 1.32.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings IntEREst_1.32.0.tar.gz
StartedAt: 2025-10-02 00:17:49 -0400 (Thu, 02 Oct 2025)
EndedAt: 2025-10-02 00:25:04 -0400 (Thu, 02 Oct 2025)
EllapsedTime: 435.5 seconds
RetCode: 0
Status:   OK  
CheckDir: IntEREst.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings IntEREst_1.32.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/IntEREst.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘IntEREst/DESCRIPTION’ ... OK
* this is package ‘IntEREst’ version ‘1.32.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'GenomicRanges', 'Rsamtools', 'SummarizedExperiment', 'edgeR',
  'S4Vectors', 'GenomicFiles'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘IntEREst’ 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'glmInterest.Rd':
  ‘[edgeR]{glmfit}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
DEXSeqIntEREst 22.401  0.231  22.635
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/IntEREst.Rcheck/00check.log’
for details.


Installation output

IntEREst.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL IntEREst
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘IntEREst’ ...
** this is package ‘IntEREst’ version ‘1.32.0’
** 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 (IntEREst)

Tests output


Example timings

IntEREst.Rcheck/IntEREst-Ex.timings

nameusersystemelapsed
DEXSeqIntEREst22.401 0.23122.635
addAnnotation0.0300.0000.029
annotateU121.8840.1642.047
applyOverlap0.1370.0000.137
attributes0.0190.0010.021
boxplot-method0.0420.0010.043
buildSsTypePwms0.0000.0000.001
counts-method0.0230.0020.025
deseqInterest3.6780.0013.679
exactTestInterest0.0740.0030.076
getRepeatTable000
glmInterest0.0870.0000.087
interest1.1930.0011.194
interest.sequential1.0250.0011.025
interestResult0.0170.0080.025
interestResultIntEx0.1490.0040.152
intexIndex0.0030.0000.003
lfc0.1940.0090.202
mergeInterestResult0.0650.0050.070
plot-method0.2910.0250.316
psi0.6420.0170.660
qlfInterest0.1160.0030.120
readInterestResults0.0260.0030.030
referencePrepare0.9700.0050.974
subInterestResult0.0270.0020.028
treatInterest0.0840.0040.088
u12Boxplot0.0480.0000.049
u12BoxplotNb0.0600.0010.062
u12DensityPlot0.2220.0030.227
u12Index0.0030.0010.005
u12NbIndex0.0370.0020.039
unionRefTr0.0130.0000.012
updateRowDataCol0.0420.0010.043