Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-21 11:38 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 734/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.64.0  (landing page)
Mark Robinson , Riccardo Romoli
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/flagme
git_branch: RELEASE_3_21
git_last_commit: a8ea6b3
git_last_commit_date: 2025-04-15 09:43:46 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'CAMERA' which is only available as a source package that needs compilation
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  NO, package depends on 'CAMERA' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for flagme on nebbiolo1

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: 1.64.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings flagme_1.64.0.tar.gz
StartedAt: 2025-08-20 22:32:09 -0400 (Wed, 20 Aug 2025)
EndedAt: 2025-08-20 22:49:08 -0400 (Wed, 20 Aug 2025)
EllapsedTime: 1018.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flagme.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings flagme_1.64.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.64.0’
* 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                           97.197 19.579  62.386
addXCMSPeaks                               50.672 10.220  44.942
corPrt                                     46.550  9.856  39.915
progressiveAlignment-class                 46.118  9.590  39.433
peaksAlignment-class                       47.542  7.908  39.528
dynRT                                      44.653 10.071  38.143
plotFrags                                  44.800  9.767  39.293
plotAlignment-peaksAlignment-method        45.380  9.172  39.250
ndpRT                                      43.116  9.397  36.673
retFatMatrix                               44.234  8.029  37.122
imputePeaks                                10.062  0.496  10.563
plotChrom-peaksDataset-method               7.997  0.659   8.656
calcTimeDiffs                               7.815  0.675   8.492
gatherInfo                                  7.420  0.576   7.998
peaksDataset                                7.255  0.588   7.844
rmaFitUnit                                  6.857  0.116   6.975
dp                                          6.338  0.530   6.868
clusterAlignment                            6.401  0.405   6.806
multipleAlignment-class                     5.987  0.250   6.237
plotClustAlignment-clusterAlignment-method  5.866  0.085   5.952
normDotProduct                              5.505  0.218   5.724
addAMDISPeaks                               5.181  0.256   5.440
* 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-3.21-bioc/meat/flagme.Rcheck/00check.log’
for details.


Installation output

flagme.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL flagme
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘flagme’ ...
** this is package ‘flagme’ version ‘1.64.0’
** 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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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
addAMDISPeaks5.1810.2565.440
addChromaTOFPeaks4.2140.1304.344
addXCMSPeaks50.67210.22044.942
betweenAlignment000
calcTimeDiffs7.8150.6758.492
clusterAlignment6.4010.4056.806
corPrt46.550 9.85639.915
dp6.3380.5306.868
dynRT44.65310.07138.143
gatherInfo7.4200.5767.998
imputePeaks10.062 0.49610.563
multipleAlignment-class5.9870.2506.237
ndpRT43.116 9.39736.673
normDotProduct5.5050.2185.724
parseChromaTOF2.0650.0052.077
parseELU1.7840.0011.792
peaksAlignment-class47.542 7.90839.528
peaksDataset7.2550.5887.844
plotAlignedFrags97.19719.57962.386
plotAlignment-peaksAlignment-method45.380 9.17239.250
plotChrom-peaksDataset-method7.9970.6598.656
plotClustAlignment-clusterAlignment-method5.8660.0855.952
plotFrags44.800 9.76739.293
plotImage4.1690.3044.474
progressiveAlignment-class46.118 9.59039.433
retFatMatrix44.234 8.02937.122
rmaFitUnit6.8570.1166.975