Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-11 11:42 -0400 (Mon, 11 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 734/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flagme 1.64.0 (landing page) Mark Robinson
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | TIMEOUT | skipped | ||||||||||
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: 1.64.0 |
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 |
############################################################################## ############################################################################## ### ### 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.
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)
flagme.Rcheck/flagme-Ex.timings
name | user | system | elapsed | |
addAMDISPeaks | 7.98 | 0.28 | 10.45 | |
addChromaTOFPeaks | 4.18 | 0.20 | 4.39 | |
addXCMSPeaks | 28.07 | 1.34 | 89.88 | |
betweenAlignment | 0 | 0 | 0 | |
calcTimeDiffs | 9.90 | 0.55 | 24.12 | |
clusterAlignment | 6.60 | 0.44 | 7.00 | |
corPrt | 28.26 | 1.36 | 89.36 | |
dp | 6.75 | 0.25 | 6.98 | |
dynRT | 24.30 | 1.39 | 86.33 | |
gatherInfo | 7.86 | 0.26 | 8.11 | |
imputePeaks | 13.30 | 0.47 | 16.96 | |
multipleAlignment-class | 9.64 | 0.36 | 9.98 | |
ndpRT | 25.87 | 1.33 | 95.00 | |
normDotProduct | 8.50 | 0.27 | 8.78 | |
parseChromaTOF | 3.19 | 0.01 | 3.28 | |
parseELU | 2.58 | 0.02 | 2.59 | |
peaksAlignment-class | 25.80 | 1.39 | 87.30 | |
peaksDataset | 8.56 | 0.33 | 8.87 | |
plotAlignedFrags | 48.58 | 2.31 | 112.88 | |
plotAlignment-peaksAlignment-method | 22.73 | 1.33 | 81.92 | |
plotChrom-peaksDataset-method | 10.60 | 0.46 | 11.05 | |
plotClustAlignment-clusterAlignment-method | 7.61 | 0.30 | 7.87 | |
plotFrags | 23.37 | 1.10 | 80.63 | |
plotImage | 5.13 | 0.21 | 5.31 | |
progressiveAlignment-class | 25.31 | 1.39 | 84.47 | |
retFatMatrix | 25.44 | 0.99 | 83.90 | |
rmaFitUnit | 9.54 | 0.48 | 10.02 | |