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This page was generated on 2025-08-06 13:52 -0400 (Wed, 06 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4813
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 727/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.65.0  (landing page)
Mark Robinson , Riccardo Romoli
Snapshot Date: 2025-08-05 13:25 -0400 (Tue, 05 Aug 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 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  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 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  NO, package depends on 'CAMERA' which is only available as a source package that needs compilation


CHECK results for flagme on nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings flagme_1.65.0.tar.gz
StartedAt: 2025-08-05 22:27:54 -0400 (Tue, 05 Aug 2025)
EndedAt: 2025-08-05 22:44:14 -0400 (Tue, 05 Aug 2025)
EllapsedTime: 980.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flagme.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings flagme_1.65.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/flagme.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                             user system elapsed
plotAlignedFrags                           97.401 17.492  59.102
addXCMSPeaks                               50.055  9.900  43.619
peaksAlignment-class                       48.245  8.760  40.043
dynRT                                      47.387  8.560  38.501
corPrt                                     47.972  7.565  38.460
ndpRT                                      44.713  7.908  36.505
retFatMatrix                               43.201  8.388  36.583
progressiveAlignment-class                 42.672  7.732  35.375
plotAlignment-peaksAlignment-method        42.139  7.298  34.205
plotFrags                                  40.862  8.490  34.851
imputePeaks                                10.957  0.112  11.076
calcTimeDiffs                               7.580  0.279   7.860
plotChrom-peaksDataset-method               7.512  0.280   7.794
gatherInfo                                  7.450  0.233   7.683
multipleAlignment-class                     7.292  0.058   7.349
dp                                          6.590  0.187   6.777
clusterAlignment                            6.442  0.139   6.584
rmaFitUnit                                  6.491  0.071   6.564
normDotProduct                              5.545  0.059   5.604
peaksDataset                                5.357  0.217   5.574
addAMDISPeaks                               5.306  0.164   5.477
plotImage                                   4.673  0.644   5.317
plotClustAlignment-clusterAlignment-method  5.102  0.069   5.171
* 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 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/flagme.Rcheck/00check.log’
for details.


Installation output

flagme.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL flagme
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘flagme’ ...
** this is package ‘flagme’ version ‘1.65.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c dp.c -o dp.o
dp.c: In function ‘dp’:
dp.c:264:35: warning: ‘tb’ may be used uninitialized [-Wmaybe-uninitialized]
  264 |           phi[(i+1)+(j+1)*(nr+1)] = tb;
      |           ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
dp.c:217:30: note: ‘tb’ was declared here
  217 |   int i,j, nr=*nr_, nc=*nc_, tb, count=0, done=0;
      |                              ^~
dp.c:263:33: warning: ‘cur_min’ may be used uninitialized [-Wmaybe-uninitialized]
  263 |           D[(i+1)+(j+1)*(nr+1)] = cur_min;
      |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
dp.c:218:21: note: ‘cur_min’ was declared here
  218 |   double gap=*gap_, cur_min, a, b, c;
      |                     ^~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c pearson.c -o pearson.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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
addAMDISPeaks5.3060.1645.477
addChromaTOFPeaks3.2580.1183.376
addXCMSPeaks50.055 9.90043.619
betweenAlignment000
calcTimeDiffs7.5800.2797.860
clusterAlignment6.4420.1396.584
corPrt47.972 7.56538.460
dp6.5900.1876.777
dynRT47.387 8.56038.501
gatherInfo7.4500.2337.683
imputePeaks10.957 0.11211.076
multipleAlignment-class7.2920.0587.349
ndpRT44.713 7.90836.505
normDotProduct5.5450.0595.604
parseChromaTOF1.9790.0031.983
parseELU1.780.001.78
peaksAlignment-class48.245 8.76040.043
peaksDataset5.3570.2175.574
plotAlignedFrags97.40117.49259.102
plotAlignment-peaksAlignment-method42.139 7.29834.205
plotChrom-peaksDataset-method7.5120.2807.794
plotClustAlignment-clusterAlignment-method5.1020.0695.171
plotFrags40.862 8.49034.851
plotImage4.6730.6445.317
progressiveAlignment-class42.672 7.73235.375
retFatMatrix43.201 8.38836.583
rmaFitUnit6.4910.0716.564