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This page was generated on 2024-07-09 17:43 -0400 (Tue, 09 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4709
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 1050/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IntEREst 1.28.0  (landing page)
Ali Oghabian , Mikko Frilander
Snapshot Date: 2024-07-07 14:00 -0400 (Sun, 07 Jul 2024)
git_url: https://git.bioconductor.org/packages/IntEREst
git_branch: RELEASE_3_19
git_last_commit: 9b139fc
git_last_commit_date: 2024-04-30 10:56:44 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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


CHECK results for IntEREst on kjohnson1

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: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2024-07-08 23:21:56 -0400 (Mon, 08 Jul 2024)
EndedAt: 2024-07-08 23:28:51 -0400 (Mon, 08 Jul 2024)
EllapsedTime: 414.3 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/IntEREst.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IntEREst/DESCRIPTION’ ... OK
* this is package ‘IntEREst’ version ‘1.28.0’
* 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 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 ... NOTE
interestIntExAnalyseSingleStranded: no visible global function
  definition for ‘bamFlagAsBitMatrix’
Undefined global functions or variables:
  bamFlagAsBitMatrix
* checking Rd files ... NOTE
checkRd: (-1) interest.Rd:105: Lost braces; missing escapes or markup?
   105 | regions to a different region defined in {limitRanges}. It is useful to ignore 
       |                                          ^
checkRd: (-1) interest.sequential.Rd:103: Lost braces; missing escapes or markup?
   103 | regions to a different region defined in {limitRanges}. It is useful to ignore 
       |                                          ^
* 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 26.341  0.192  26.599
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-arm64/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
DEXSeqIntEREst26.341 0.19226.599
addAnnotation0.0330.0020.035
annotateU122.0460.1122.160
applyOverlap0.1490.0010.150
attributes0.0210.0030.025
boxplot-method0.0720.0010.073
buildSsTypePwms0.0000.0000.001
counts-method0.0280.0020.030
deseqInterest4.1470.0164.173
exactTestInterest0.0860.0020.088
getRepeatTable000
glmInterest0.1180.0010.119
interest1.2810.0171.300
interest.sequential1.0350.0091.044
interestResult0.0160.0010.017
interestResultIntEx0.1580.0020.160
intexIndex0.0030.0000.003
lfc0.2280.0030.234
mergeInterestResult0.0600.0010.060
plot-method0.3050.0060.315
psi0.6060.0040.610
qlfInterest0.0970.0060.104
readInterestResults0.0150.0020.017
referencePrepare0.7460.0220.777
subInterestResult0.0360.0010.038
treatInterest0.1160.0040.120
u12Boxplot0.0540.0020.055
u12BoxplotNb0.0750.0010.076
u12DensityPlot0.230.010.24
u12Index0.0050.0000.005
u12NbIndex0.0380.0010.040
unionRefTr0.0140.0000.015
updateRowDataCol0.0510.0020.053