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This page was generated on 2025-10-03 12:04 -0400 (Fri, 03 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 735/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.65.0  (landing page)
Mark Robinson , Riccardo Romoli
Snapshot Date: 2025-10-02 13:45 -0400 (Thu, 02 Oct 2025)
git_url: https://git.bioconductor.org/packages/flagme
git_branch: devel
git_last_commit: 2a39fc4
git_last_commit_date: 2025-04-15 09:43:46 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'CAMERA' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  NO, package depends on 'CAMERA' which is only available as a source package that needs compilation
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for flagme on lconway

To the developers/maintainers of the flagme package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flagme.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: flagme
Version: 1.65.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flagme_1.65.0.tar.gz
StartedAt: 2025-10-02 21:29:32 -0400 (Thu, 02 Oct 2025)
EndedAt: 2025-10-02 21:45:33 -0400 (Thu, 02 Oct 2025)
EllapsedTime: 961.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flagme.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flagme_1.65.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/flagme.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.65.0’
* package encoding: UTF-8
* 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 ‘flagme’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘xcms:::rectUnique’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addXCMSPeaks: no visible global function definition for ‘bpparam’
addXCMSPeaks: no visible global function definition for ‘sampnames’
addXCMSPeaks : <anonymous> : <anonymous>: no visible global function
  definition for ‘setNames’
importSpec : <anonymous>: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  bpparam sampnames setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'addXCMSPeaks.Rd':
  ‘[xcms]{findPeaks-matchedFilter}’ ‘[xcms]{findPeaks-centWave}’
  ‘[xcms]{peaksDataset}’

Missing link(s) in Rd file 'plotAlignment-peaksAlignment-method.Rd':
  ‘plotAlignment’

Missing link(s) in Rd file 'plotClustAlignment-clusterAlignment-method.Rd':
  ‘plotAlignment’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotAlignment-peaksAlignment-method.Rd: plotAlignment
  plotClustAlignment-clusterAlignment-method.Rd: plotAlignment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘plotAlignment’ ‘plotChrom’ ‘plotClustAlignment’
Undocumented S4 methods:
  generic 'show' and siglist 'betweenAlignment'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                              user system elapsed
plotAlignedFrags                           102.376 24.843  63.512
addXCMSPeaks                                59.240 12.042  50.632
corPrt                                      53.327 12.703  45.223
peaksAlignment-class                        52.777 12.113  45.144
dynRT                                       51.700 12.239  43.597
retFatMatrix                                50.693 12.590  43.880
ndpRT                                       49.314 12.039  42.221
plotAlignment-peaksAlignment-method         49.035 11.782  42.077
progressiveAlignment-class                  49.238 11.469  41.817
plotFrags                                   49.012 11.617  41.723
imputePeaks                                 12.275  0.313  12.783
plotChrom-peaksDataset-method                9.542  0.297   9.947
gatherInfo                                   8.614  0.257   8.956
multipleAlignment-class                      8.624  0.221   8.993
rmaFitUnit                                   8.266  0.295   8.647
calcTimeDiffs                                8.023  0.379   8.513
dp                                           7.863  0.223   8.160
plotClustAlignment-clusterAlignment-method   7.075  0.183   7.342
clusterAlignment                             6.359  0.186   6.623
normDotProduct                               6.327  0.213   6.608
addAMDISPeaks                                6.285  0.207   6.556
peaksDataset                                 5.955  0.212   6.244
addChromaTOFPeaks                            5.045  0.161   5.236
plotImage                                    4.926  0.158   5.144
* 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: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/flagme.Rcheck/00check.log’
for details.


Installation output

flagme.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘flagme’ ...
** this is package ‘flagme’ version ‘1.65.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c dp.c -o dp.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pearson.c -o pearson.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o flagme.so dp.o init.o pearson.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-flagme/00new/flagme/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flagme)

Tests output


Example timings

flagme.Rcheck/flagme-Ex.timings

nameusersystemelapsed
addAMDISPeaks6.2850.2076.556
addChromaTOFPeaks5.0450.1615.236
addXCMSPeaks59.24012.04250.632
betweenAlignment0.0010.0010.001
calcTimeDiffs8.0230.3798.513
clusterAlignment6.3590.1866.623
corPrt53.32712.70345.223
dp7.8630.2238.160
dynRT51.70012.23943.597
gatherInfo8.6140.2578.956
imputePeaks12.275 0.31312.783
multipleAlignment-class8.6240.2218.993
ndpRT49.31412.03942.221
normDotProduct6.3270.2136.608
parseChromaTOF2.7460.0332.810
parseELU2.2770.0222.325
peaksAlignment-class52.77712.11345.144
peaksDataset5.9550.2126.244
plotAlignedFrags102.376 24.843 63.512
plotAlignment-peaksAlignment-method49.03511.78242.077
plotChrom-peaksDataset-method9.5420.2979.947
plotClustAlignment-clusterAlignment-method7.0750.1837.342
plotFrags49.01211.61741.723
plotImage4.9260.1585.144
progressiveAlignment-class49.23811.46941.817
retFatMatrix50.69312.59043.880
rmaFitUnit8.2660.2958.647