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This page was generated on 2025-08-11 11:42 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
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: 2025-08-07 13:40 -0400 (Thu, 07 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 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  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    TIMEOUT  skipped


CHECK results for flagme on palomino7

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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flagme.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings flagme_1.64.0.tar.gz
StartedAt: 2025-08-08 01:52:19 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 02:16:16 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 1437.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flagme.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flagme.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings flagme_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/flagme.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 whether package 'flagme' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* 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 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/flagme/libs/x64/flagme.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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                           48.58   2.31  112.88
corPrt                                     28.26   1.36   89.36
addXCMSPeaks                               28.07   1.34   89.88
ndpRT                                      25.87   1.33   95.00
peaksAlignment-class                       25.80   1.39   87.30
progressiveAlignment-class                 25.31   1.39   84.47
retFatMatrix                               25.44   0.99   83.90
dynRT                                      24.30   1.39   86.33
plotFrags                                  23.37   1.10   80.63
plotAlignment-peaksAlignment-method        22.73   1.33   81.92
imputePeaks                                13.30   0.47   16.96
plotChrom-peaksDataset-method              10.60   0.46   11.05
calcTimeDiffs                               9.90   0.55   24.12
rmaFitUnit                                  9.54   0.48   10.02
multipleAlignment-class                     9.64   0.36    9.98
peaksDataset                                8.56   0.33    8.87
normDotProduct                              8.50   0.27    8.78
addAMDISPeaks                               7.98   0.28   10.45
gatherInfo                                  7.86   0.26    8.11
plotClustAlignment-clusterAlignment-method  7.61   0.30    7.87
clusterAlignment                            6.60   0.44    7.00
dp                                          6.75   0.25    6.98
plotImage                                   5.13   0.21    5.31
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/flagme.Rcheck/00check.log'
for details.


Installation output

flagme.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL flagme
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'flagme' ...
** this is package 'flagme' version '1.64.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -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  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c init.c -o init.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c pearson.c -o pearson.o
gcc -shared -s -static-libgcc -o flagme.dll tmp.def dp.o init.o pearson.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-flagme/00new/flagme/libs/x64
** 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 (flagme)

Tests output


Example timings

flagme.Rcheck/flagme-Ex.timings

nameusersystemelapsed
addAMDISPeaks 7.98 0.2810.45
addChromaTOFPeaks4.180.204.39
addXCMSPeaks28.07 1.3489.88
betweenAlignment000
calcTimeDiffs 9.90 0.5524.12
clusterAlignment6.600.447.00
corPrt28.26 1.3689.36
dp6.750.256.98
dynRT24.30 1.3986.33
gatherInfo7.860.268.11
imputePeaks13.30 0.4716.96
multipleAlignment-class9.640.369.98
ndpRT25.87 1.3395.00
normDotProduct8.500.278.78
parseChromaTOF3.190.013.28
parseELU2.580.022.59
peaksAlignment-class25.80 1.3987.30
peaksDataset8.560.338.87
plotAlignedFrags 48.58 2.31112.88
plotAlignment-peaksAlignment-method22.73 1.3381.92
plotChrom-peaksDataset-method10.60 0.4611.05
plotClustAlignment-clusterAlignment-method7.610.307.87
plotFrags23.37 1.1080.63
plotImage5.130.215.31
progressiveAlignment-class25.31 1.3984.47
retFatMatrix25.44 0.9983.90
rmaFitUnit 9.54 0.4810.02