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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1036/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IntEREst 1.31.0  (landing page)
Ali Oghabian
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/IntEREst
git_branch: devel
git_last_commit: 99f6377
git_last_commit_date: 2024-10-29 10:17:53 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  NO, package depends on 'DEXSeq' which is not available
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'DEXSeq' which is not available
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'DEXSeq' which is not available
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'DEXSeq' which is not available
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


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: 1.31.0
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_1.31.0.tar.gz
StartedAt: 2024-12-23 23:05:46 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 23:12:43 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 417.5 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_1.31.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/IntEREst.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘IntEREst/DESCRIPTION’ ... OK
* this is package ‘IntEREst’ version ‘1.31.0’
* 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 ... 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 21.373  0.358  21.731
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/IntEREst.Rcheck/00check.log’
for details.


Installation output

IntEREst.Rcheck/00install.out

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###
### 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’ ...
** 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
DEXSeqIntEREst21.373 0.35821.731
addAnnotation0.0280.0010.029
annotateU121.7980.1361.934
applyOverlap0.1340.0000.135
attributes0.0200.0010.022
boxplot-method0.0430.0000.044
buildSsTypePwms000
counts-method0.0230.0020.025
deseqInterest3.7370.0183.756
exactTestInterest0.0740.0000.074
getRepeatTable000
glmInterest0.0850.0000.086
interest1.1760.0111.187
interest.sequential1.0570.0021.059
interestResult0.0150.0010.016
interestResultIntEx0.1490.0020.150
intexIndex0.0030.0000.002
lfc0.1810.0000.180
mergeInterestResult0.0550.0010.057
plot-method0.2720.0040.276
psi0.6070.0030.610
qlfInterest0.1140.0020.118
readInterestResults0.0240.0040.028
referencePrepare1.0300.0021.033
subInterestResult0.0250.0010.027
treatInterest0.0840.0050.088
u12Boxplot0.0480.0000.049
u12BoxplotNb0.060.000.06
u12DensityPlot0.1920.0030.196
u12Index0.0040.0000.004
u12NbIndex0.0350.0020.038
unionRefTr0.0120.0000.011
updateRowDataCol0.0390.0020.041