| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-23 11:32 -0500 (Mon, 23 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4871 |
| 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 747/2354 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flagme 1.67.0 (landing page) Mark Robinson
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
| See other builds for flagme in R Universe. | ||||||||||||||
|
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. |
| Package: flagme |
| Version: 1.67.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings flagme_1.67.0.tar.gz |
| StartedAt: 2026-02-23 00:03:28 -0500 (Mon, 23 Feb 2026) |
| EndedAt: 2026-02-23 00:21:10 -0500 (Mon, 23 Feb 2026) |
| EllapsedTime: 1061.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flagme.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings flagme_1.67.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/flagme.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘1.67.0’
* 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotAlignedFrags 97.087 19.424 62.155
plotAlignment-peaksAlignment-method 55.107 9.943 45.990
addXCMSPeaks 53.140 9.372 48.639
retFatMatrix 46.460 12.363 41.898
peaksAlignment-class 49.717 8.891 40.164
corPrt 47.628 8.477 38.427
progressiveAlignment-class 44.670 9.690 39.409
dynRT 44.442 9.550 38.630
plotFrags 44.150 7.375 36.103
ndpRT 42.530 8.399 36.248
imputePeaks 9.449 0.277 9.732
plotChrom-peaksDataset-method 8.484 0.230 8.715
multipleAlignment-class 7.165 0.344 7.510
rmaFitUnit 7.071 0.194 7.265
dp 6.733 0.330 7.063
calcTimeDiffs 6.453 0.458 6.914
gatherInfo 6.376 0.126 6.503
clusterAlignment 5.900 0.262 6.162
peaksDataset 5.674 0.234 5.908
plotClustAlignment-clusterAlignment-method 5.697 0.129 5.827
addAMDISPeaks 5.385 0.148 5.546
normDotProduct 5.382 0.109 5.490
addChromaTOFPeaks 4.786 0.408 5.193
* 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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/flagme.Rcheck/00check.log’
for details.
flagme.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL flagme
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘flagme’ ...
** this is package ‘flagme’ version ‘1.67.0’
** 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-3.23-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-3.23-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-3.23-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-3.23-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-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)
flagme.Rcheck/flagme-Ex.timings
| name | user | system | elapsed | |
| addAMDISPeaks | 5.385 | 0.148 | 5.546 | |
| addChromaTOFPeaks | 4.786 | 0.408 | 5.193 | |
| addXCMSPeaks | 53.140 | 9.372 | 48.639 | |
| betweenAlignment | 0.000 | 0.000 | 0.001 | |
| calcTimeDiffs | 6.453 | 0.458 | 6.914 | |
| clusterAlignment | 5.900 | 0.262 | 6.162 | |
| corPrt | 47.628 | 8.477 | 38.427 | |
| dp | 6.733 | 0.330 | 7.063 | |
| dynRT | 44.442 | 9.550 | 38.630 | |
| gatherInfo | 6.376 | 0.126 | 6.503 | |
| imputePeaks | 9.449 | 0.277 | 9.732 | |
| multipleAlignment-class | 7.165 | 0.344 | 7.510 | |
| ndpRT | 42.530 | 8.399 | 36.248 | |
| normDotProduct | 5.382 | 0.109 | 5.490 | |
| parseChromaTOF | 2.107 | 0.004 | 2.119 | |
| parseELU | 1.735 | 0.000 | 1.735 | |
| peaksAlignment-class | 49.717 | 8.891 | 40.164 | |
| peaksDataset | 5.674 | 0.234 | 5.908 | |
| plotAlignedFrags | 97.087 | 19.424 | 62.155 | |
| plotAlignment-peaksAlignment-method | 55.107 | 9.943 | 45.990 | |
| plotChrom-peaksDataset-method | 8.484 | 0.230 | 8.715 | |
| plotClustAlignment-clusterAlignment-method | 5.697 | 0.129 | 5.827 | |
| plotFrags | 44.150 | 7.375 | 36.103 | |
| plotImage | 4.466 | 0.119 | 4.585 | |
| progressiveAlignment-class | 44.670 | 9.690 | 39.409 | |
| retFatMatrix | 46.460 | 12.363 | 41.898 | |
| rmaFitUnit | 7.071 | 0.194 | 7.265 | |