Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:46 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 715/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flagme 1.58.0 (landing page) Mark Robinson
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.1 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: 1.58.0 |
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flagme.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings flagme_1.58.0.tar.gz |
StartedAt: 2024-04-16 00:48:47 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 01:09:03 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 1216.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: flagme.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flagme.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings flagme_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/flagme.Rcheck' * using R version 4.3.3 (2024-02-29 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * 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 '1.58.0' * 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) 12.3.0' * 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 R 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 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 documentation object 'addXCMSPeaks.Rd': '[xcms]{findPeaks-matchedFilter}' '[xcms]{findPeaks-centWave}' '[xcms]{peaksDataset}' Missing link or links in documentation object 'plotAlignment-peaksAlignment-method.Rd': 'plotAlignment' Missing link or links in documentation object '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-3.18-bioc/R/library/flagme/libs/x64/flagme.dll': 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 39.19 0.90 101.44 addXCMSPeaks 23.51 0.53 79.44 peaksAlignment-class 22.13 0.42 77.59 corPrt 22.09 0.38 76.30 plotFrags 21.94 0.36 75.45 dynRT 21.66 0.54 78.06 ndpRT 21.59 0.47 76.45 retFatMatrix 20.75 0.50 73.81 progressiveAlignment-class 20.50 0.27 74.09 plotAlignment-peaksAlignment-method 20.38 0.32 75.36 imputePeaks 10.11 0.28 10.46 plotChrom-peaksDataset-method 9.10 0.23 9.33 rmaFitUnit 7.75 0.10 8.05 calcTimeDiffs 7.02 0.25 7.26 multipleAlignment-class 6.94 0.14 7.08 gatherInfo 6.81 0.11 6.92 clusterAlignment 6.53 0.06 6.59 normDotProduct 6.43 0.13 6.55 peaksDataset 6.15 0.05 6.21 dp 6.00 0.14 6.14 addAMDISPeaks 5.83 0.07 6.06 plotClustAlignment-clusterAlignment-method 5.57 0.09 5.67 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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-3.18-bioc/meat/flagme.Rcheck/00check.log' for details.
flagme.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL flagme ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library' * installing *source* package 'flagme' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.3.0' gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/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: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; | ^~~~~~~ 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; | ^~ gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/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:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.18-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 | 5.83 | 0.07 | 6.06 | |
addChromaTOFPeaks | 3.34 | 0.16 | 3.75 | |
addXCMSPeaks | 23.51 | 0.53 | 79.44 | |
betweenAlignment | 0 | 0 | 0 | |
calcTimeDiffs | 7.02 | 0.25 | 7.26 | |
clusterAlignment | 6.53 | 0.06 | 6.59 | |
corPrt | 22.09 | 0.38 | 76.30 | |
dp | 6.00 | 0.14 | 6.14 | |
dynRT | 21.66 | 0.54 | 78.06 | |
gatherInfo | 6.81 | 0.11 | 6.92 | |
imputePeaks | 10.11 | 0.28 | 10.46 | |
multipleAlignment-class | 6.94 | 0.14 | 7.08 | |
ndpRT | 21.59 | 0.47 | 76.45 | |
normDotProduct | 6.43 | 0.13 | 6.55 | |
parseChromaTOF | 2.81 | 0.00 | 2.96 | |
parseELU | 1.84 | 0.00 | 1.85 | |
peaksAlignment-class | 22.13 | 0.42 | 77.59 | |
peaksDataset | 6.15 | 0.05 | 6.21 | |
plotAlignedFrags | 39.19 | 0.90 | 101.44 | |
plotAlignment-peaksAlignment-method | 20.38 | 0.32 | 75.36 | |
plotChrom-peaksDataset-method | 9.10 | 0.23 | 9.33 | |
plotClustAlignment-clusterAlignment-method | 5.57 | 0.09 | 5.67 | |
plotFrags | 21.94 | 0.36 | 75.45 | |
plotImage | 3.55 | 0.05 | 3.71 | |
progressiveAlignment-class | 20.50 | 0.27 | 74.09 | |
retFatMatrix | 20.75 | 0.50 | 73.81 | |
rmaFitUnit | 7.75 | 0.10 | 8.05 | |