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This page was generated on 2025-08-25 12:07 -0400 (Mon, 25 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 1059/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IPO 1.35.0  (landing page)
Thomas Lieb
Snapshot Date: 2025-08-24 13:45 -0400 (Sun, 24 Aug 2025)
git_url: https://git.bioconductor.org/packages/IPO
git_branch: devel
git_last_commit: cb37025
git_last_commit_date: 2025-04-15 11:04:15 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK results for IPO on taishan

To the developers/maintainers of the IPO package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IPO.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: IPO
Version: 1.35.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:IPO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings IPO_1.35.0.tar.gz
StartedAt: 2025-08-22 09:09:41 -0000 (Fri, 22 Aug 2025)
EndedAt: 2025-08-22 09:49:42 -0000 (Fri, 22 Aug 2025)
EllapsedTime: 2400.8 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: IPO.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:IPO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings IPO_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/IPO.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IPO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IPO’ version ‘1.35.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IPO’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* 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 ... 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
calcPPS 3.461  0.112   6.668
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’

Installation output

IPO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL IPO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘IPO’ ...
** this is package ‘IPO’ version ‘1.35.0’
** using staged installation
** R
** 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 (IPO)

Tests output

IPO.Rcheck/tests/runTests.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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.

> library("msdata")
> 
> BiocGenerics:::testPackage("IPO")

This is xcms version 4.7.2 


Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.




starting new DoE with:
min_peakwidth: c(3, 9.5)
max_peakwidth: c(10, 20)
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE

1
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 235 found.

2
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!

3
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 88 found.

4
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!

5
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found.

6
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 215 found.

7
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!

8
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 149 found.

9
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 101 found.

10
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found.


Example timings

IPO.Rcheck/IPO-Ex.timings

nameusersystemelapsed
IPO-package0.0000.0000.001
attachList0.0010.0000.000
calcPPS3.4610.1126.668
calculateXcmsSet2.3900.8273.687
combineParams0.0150.0040.019
createModel2.9990.8420.099
decode0.0010.0000.001
findIsotopes.CAMERA2.6010.8533.360
findIsotopes.IPO3.4731.1614.542
getBbdParameter0.0030.0000.003
getCcdParameter0.0010.0070.008
getDefaultRetCorCenterSample0.0000.0010.000
getDefaultRetGroupStartingParams0.0010.0000.001
getDefaultXcmsSetStartingParams0.0000.0000.001
getNormalizedResponse000
getRGTVValues000
optimizeRetGroup000
optimizeXcmsSet000
toMatrix0.0010.0000.002
typeCastParams000
writeParamsTable0.0060.0000.005
writeRScript0.0020.0000.002