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This page was generated on 2025-10-11 12:04 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
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 736/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.65.0  (landing page)
Mark Robinson , Riccardo Romoli
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 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: 2025-10-10 21:52:33 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 22:11:46 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 1153.0 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                           96.278 26.320  75.116
corPrt                                     55.088 17.088  58.575
plotFrags                                  52.687 17.651  73.777
dynRT                                      56.035 13.569  48.187
addXCMSPeaks                               54.635 14.378  59.780
progressiveAlignment-class                 52.814 15.787  58.000
plotAlignment-peaksAlignment-method        49.235 15.917  62.821
peaksAlignment-class                       50.269 14.522  52.914
retFatMatrix                               50.092 14.100  47.230
ndpRT                                      50.037 13.607  49.632
imputePeaks                                11.134  0.307  11.539
plotChrom-peaksDataset-method               9.438  0.780  13.626
calcTimeDiffs                               8.522  0.556  10.770
multipleAlignment-class                     8.619  0.224   8.963
gatherInfo                                  8.418  0.321   8.885
rmaFitUnit                                  8.300  0.377   8.899
dp                                          6.930  0.268   7.322
normDotProduct                              6.732  0.302   7.168
plotClustAlignment-clusterAlignment-method  5.996  0.601  10.445
clusterAlignment                            5.917  0.405   8.660
peaksDataset                                5.848  0.345   6.729
plotImage                                   4.955  0.341   6.292
addAMDISPeaks                               4.877  0.276   6.000
* 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
addAMDISPeaks4.8770.2766.000
addChromaTOFPeaks4.5860.2084.984
addXCMSPeaks54.63514.37859.780
betweenAlignment000
calcTimeDiffs 8.522 0.55610.770
clusterAlignment5.9170.4058.660
corPrt55.08817.08858.575
dp6.9300.2687.322
dynRT56.03513.56948.187
gatherInfo8.4180.3218.885
imputePeaks11.134 0.30711.539
multipleAlignment-class8.6190.2248.963
ndpRT50.03713.60749.632
normDotProduct6.7320.3027.168
parseChromaTOF3.1710.0693.301
parseELU2.5910.0342.676
peaksAlignment-class50.26914.52252.914
peaksDataset5.8480.3456.729
plotAlignedFrags96.27826.32075.116
plotAlignment-peaksAlignment-method49.23515.91762.821
plotChrom-peaksDataset-method 9.438 0.78013.626
plotClustAlignment-clusterAlignment-method 5.996 0.60110.445
plotFrags52.68717.65173.777
plotImage4.9550.3416.292
progressiveAlignment-class52.81415.78758.000
retFatMatrix50.09214.10047.230
rmaFitUnit8.3000.3778.899