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This page was generated on 2024-03-04 11:37:28 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1036/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IntEREst 1.26.0  (landing page)
Ali Oghabian , Mikko Frilander
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/IntEREst
git_branch: RELEASE_3_18
git_last_commit: 759bac6
git_last_commit_date: 2023-10-24 10:55:57 -0500 (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
lconwaymacOS 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 IntEREst on lconway


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: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IntEREst_1.26.0.tar.gz
StartedAt: 2024-03-03 21:18:07 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 21:25:23 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 435.9 seconds
RetCode: 0
Status:   OK  
CheckDir: IntEREst.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IntEREst_1.26.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/IntEREst.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IntEREst/DESCRIPTION’ ... OK
* this is package ‘IntEREst’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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 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 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
interestIntExAnalyseSingleStranded: no visible global function
  definition for ‘bamFlagAsBitMatrix’
Undefined global functions or variables:
  bamFlagAsBitMatrix
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
DEXSeqIntEREst 24.136  0.317  24.595
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/IntEREst.Rcheck/00check.log’
for details.



Installation output

IntEREst.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘IntEREst’ ...
** 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
DEXSeqIntEREst24.136 0.31724.595
addAnnotation0.0360.0010.037
annotateU122.4420.1392.637
applyOverlap0.1380.0010.140
attributes0.0220.0020.023
boxplot-method0.0430.0010.045
buildSsTypePwms0.0000.0000.001
counts-method0.0230.0010.024
deseqInterest4.6890.0554.768
exactTestInterest0.1590.0030.163
getRepeatTable000
glmInterest0.1280.0030.133
interest1.5080.0231.540
interest.sequential1.3650.0161.386
interestResult0.0210.0010.022
interestResultIntEx0.2050.0030.208
intexIndex0.0030.0000.003
lfc0.2180.0050.225
mergeInterestResult0.0780.0020.081
plot-method0.3560.0090.367
psi0.7360.0070.749
qlfInterest0.1570.0050.163
readInterestResults0.0340.0040.038
referencePrepare1.2140.0171.237
subInterestResult0.0400.0020.043
treatInterest0.1250.0040.129
u12Boxplot0.0630.0010.064
u12BoxplotNb0.0700.0010.071
u12DensityPlot0.1910.0080.200
u12Index0.0030.0000.004
u12NbIndex0.0320.0010.032
unionRefTr0.010.000.01
updateRowDataCol0.0480.0020.050