Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:03 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the flagme package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 673/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flagme 1.55.0 (landing page) Mark Robinson
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: flagme |
Version: 1.55.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings flagme_1.55.0.tar.gz |
StartedAt: 2023-02-07 01:40:29 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 01:57:58 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 1049.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: flagme.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings flagme_1.55.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/flagme.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘flagme/DESCRIPTION’ ... OK * this is package ‘flagme’ version ‘1.55.0’ * 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 11.3.0-1ubuntu1~22.04) 11.3.0’ * 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 dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘MSnbase’ Missing or unexported object: ‘xcms::rectUnique’ * 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 : <anonymous> : <anonymous>: no visible global function definition for ‘setNames’ importSpec : <anonymous>: no visible global function definition for ‘setNames’ Undefined global functions or variables: bpparam 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 '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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘flagme-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plotAlignedFrags > ### Title: plotAlignedFrags > ### Aliases: plotAlignedFrags > ### Keywords: gatherInfo() plot() > > ### ** Examples > > > files <- list.files(path = paste(find.package("gcspikelite"), "data", + sep = "/"),"CDF", full = TRUE) > data <- peaksDataset(files[1:4], mz = seq(50, 550), rtrange = c(7.5, 8.5)) Reading /home/biocbuild/bbs-3.17-bioc/R/library/gcspikelite/data/0709_468.CDF Create profile matrix with method 'bin' and step 1 ... OK Reading /home/biocbuild/bbs-3.17-bioc/R/library/gcspikelite/data/0709_470.CDF Create profile matrix with method 'bin' and step 1 ... OK Reading /home/biocbuild/bbs-3.17-bioc/R/library/gcspikelite/data/0709_471.CDF Create profile matrix with method 'bin' and step 1 ... OK Reading /home/biocbuild/bbs-3.17-bioc/R/library/gcspikelite/data/0709_474.CDF Create profile matrix with method 'bin' and step 1 ... OK > ## create settings object > mfp <- xcms::MatchedFilterParam(fwhm = 10, snthresh = 5) > cwt <- xcms::CentWaveParam(snthresh = 3, ppm = 3000, peakwidth = c(3, 40), + prefilter = c(3, 100), fitgauss = FALSE, integrate = 2, noise = 0, + extendLengthMSW = TRUE, mzCenterFun = "wMean") > data <- addXCMSPeaks(files[1:4], data, settings = mfp, minintens = 100, + multipleMatchedFilter = FALSE, multipleMatchedFilterParam = + list(fwhm = c(5, 10, 20), rt_abs = 3, mz_abs = 0.1)) Start peakPicking Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method. Error in reducer$value.cache[[as.character(idx)]] <- values : wrong args for environment subassignment Calls: addXCMSPeaks ... .bploop_impl -> .collect_result -> .reducer_add -> .reducer_add Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘flagme-knitr.Rnw’ using ‘UTF-8’... OK ‘flagme.Rnw’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘flagme-knitr.Rnw’ using Sweave Loading required package: gcspikelite Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: ProtGenerics Attaching package: ‘ProtGenerics’ The following object is masked from ‘package:stats’: smooth This is MSnbase version 2.25.1 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: ‘MSnbase’ The following object is masked from ‘package:base’: trimws This is xcms version 3.21.0 Attaching package: ‘xcms’ The following object is masked from ‘package:stats’: sigma Loading required package: CAMERA Attaching package: ‘flagme’ The following object is masked from ‘package:xcms’: plotChrom Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method. Error: processing vignette 'flagme-knitr.Rnw' failed with diagnostics: chunk 3 (label = addXCMS) Error in reducer$value.cache[[as.character(idx)]] <- values : wrong args for environment subassignment --- failed re-building ‘flagme-knitr.Rnw’ --- re-building ‘flagme.Rnw’ using Sweave Loading required package: gcspikelite Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: ProtGenerics Attaching package: ‘ProtGenerics’ The following object is masked from ‘package:stats’: smooth This is MSnbase version 2.25.1 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: ‘MSnbase’ The following object is masked from ‘package:base’: trimws This is xcms version 3.21.0 Attaching package: ‘xcms’ The following object is masked from ‘package:stats’: sigma Loading required package: CAMERA Attaching package: ‘flagme’ The following object is masked from ‘package:xcms’: plotChrom Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method. Processing 3339 mz slices ... OK Defining peak areas for filling-in ... OK Start integrating peak areas from original files Requesting 193 peaks from 0709_474.CDF ... got 188. Requesting 218 peaks from 0709_468.CDF ... got 210. Requesting 169 peaks from 0709_475.CDF ... got 166. Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. --- finished re-building ‘flagme.Rnw’ SUMMARY: processing the following file failed: ‘flagme-knitr.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/flagme.Rcheck/00check.log’ for details.
flagme.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL flagme ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘flagme’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c dp.c -o dp.o dp.c: In function ‘dp’: dp.c:263:33: warning: ‘cur_min’ may be used uninitialized in this function [-Wmaybe-uninitialized] 263 | D[(i+1)+(j+1)*(nr+1)] = cur_min; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ dp.c:264:35: warning: ‘tb’ may be used uninitialized in this function [-Wmaybe-uninitialized] 264 | phi[(i+1)+(j+1)*(nr+1)] = tb; | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c pearson.c -o pearson.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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 | 5.322 | 0.092 | 5.645 | |
addChromaTOFPeaks | 5.882 | 0.048 | 5.935 | |
addXCMSPeaks | 57.241 | 5.345 | 46.601 | |
betweenAlignment | 0 | 0 | 0 | |
calcTimeDiffs | 8.941 | 0.302 | 9.368 | |
clusterAlignment | 7.553 | 0.040 | 7.642 | |
corPrt | 52.604 | 5.270 | 41.930 | |
dp | 6.660 | 0.247 | 6.910 | |
dynRT | 56.914 | 5.483 | 44.910 | |
gatherInfo | 7.578 | 0.048 | 7.632 | |
imputePeaks | 12.093 | 0.072 | 12.358 | |
multipleAlignment-class | 7.474 | 0.048 | 7.529 | |
ndpRT | 53.294 | 5.859 | 70.523 | |
normDotProduct | 6.878 | 0.077 | 13.649 | |
parseChromaTOF | 2.904 | 0.004 | 5.790 | |
parseELU | 2.665 | 0.007 | 3.824 | |
peaksAlignment-class | 52.447 | 5.537 | 58.272 | |
peaksDataset | 6.394 | 0.256 | 6.656 | |