Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-22 11:35:39 -0400 (Wed, 22 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
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 727/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flagme 1.60.0 (landing page) Mark Robinson
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.60.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flagme.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings flagme_1.60.0.tar.gz |
StartedAt: 2024-05-22 01:55:30 -0400 (Wed, 22 May 2024) |
EndedAt: 2024-05-22 02:16:40 -0400 (Wed, 22 May 2024) |
EllapsedTime: 1270.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: flagme.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flagme.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings flagme_1.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/flagme.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * 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 '1.60.0' * 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) 13.2.0' * 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 or links in Rd file 'addXCMSPeaks.Rd': '[xcms]{findPeaks-matchedFilter}' '[xcms]{findPeaks-centWave}' '[xcms]{peaksDataset}' Missing link or links in Rd file 'plotAlignment-peaksAlignment-method.Rd': 'plotAlignment' Missing link or links in Rd file 'plotClustAlignment-clusterAlignment-method.Rd': 'plotAlignment' See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 'F:/biocbuild/bbs-3.19-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 41.66 3.19 104.69 addXCMSPeaks 25.88 1.62 84.70 corPrt 24.26 1.62 81.84 peaksAlignment-class 23.98 1.52 79.56 dynRT 22.90 1.59 81.69 ndpRT 22.52 1.69 84.74 plotFrags 21.94 1.56 76.89 plotAlignment-peaksAlignment-method 21.87 1.56 79.70 progressiveAlignment-class 21.72 1.57 77.61 retFatMatrix 20.93 1.44 73.42 imputePeaks 11.78 0.74 14.00 plotChrom-peaksDataset-method 9.81 0.47 10.25 calcTimeDiffs 8.76 0.77 10.47 gatherInfo 8.60 0.53 9.09 multipleAlignment-class 8.59 0.34 8.92 clusterAlignment 7.66 0.41 8.05 dp 7.49 0.30 7.77 rmaFitUnit 6.39 0.97 7.33 plotClustAlignment-clusterAlignment-method 6.75 0.37 7.13 normDotProduct 6.28 0.56 6.81 addAMDISPeaks 6.61 0.15 8.05 peaksDataset 5.63 0.39 5.99 addChromaTOFPeaks 4.85 0.27 5.09 * 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 'F:/biocbuild/bbs-3.19-bioc/meat/flagme.Rcheck/00check.log' for details.
flagme.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL flagme ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'flagme' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.19-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 | 6.61 | 0.15 | 8.05 | |
addChromaTOFPeaks | 4.85 | 0.27 | 5.09 | |
addXCMSPeaks | 25.88 | 1.62 | 84.70 | |
betweenAlignment | 0 | 0 | 0 | |
calcTimeDiffs | 8.76 | 0.77 | 10.47 | |
clusterAlignment | 7.66 | 0.41 | 8.05 | |
corPrt | 24.26 | 1.62 | 81.84 | |
dp | 7.49 | 0.30 | 7.77 | |
dynRT | 22.90 | 1.59 | 81.69 | |
gatherInfo | 8.60 | 0.53 | 9.09 | |
imputePeaks | 11.78 | 0.74 | 14.00 | |
multipleAlignment-class | 8.59 | 0.34 | 8.92 | |
ndpRT | 22.52 | 1.69 | 84.74 | |
normDotProduct | 6.28 | 0.56 | 6.81 | |
parseChromaTOF | 3.59 | 0.08 | 4.92 | |
parseELU | 2.41 | 0.01 | 2.42 | |
peaksAlignment-class | 23.98 | 1.52 | 79.56 | |
peaksDataset | 5.63 | 0.39 | 5.99 | |
plotAlignedFrags | 41.66 | 3.19 | 104.69 | |
plotAlignment-peaksAlignment-method | 21.87 | 1.56 | 79.70 | |
plotChrom-peaksDataset-method | 9.81 | 0.47 | 10.25 | |
plotClustAlignment-clusterAlignment-method | 6.75 | 0.37 | 7.13 | |
plotFrags | 21.94 | 1.56 | 76.89 | |
plotImage | 3.69 | 0.21 | 3.89 | |
progressiveAlignment-class | 21.72 | 1.57 | 77.61 | |
retFatMatrix | 20.93 | 1.44 | 73.42 | |
rmaFitUnit | 6.39 | 0.97 | 7.33 | |