Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:40 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 266/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAMERA 1.61.0 (landing page) Steffen Neumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the CAMERA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAMERA.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: CAMERA |
Version: 1.61.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAMERA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CAMERA_1.61.0.tar.gz |
StartedAt: 2024-08-20 23:03:47 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 23:25:46 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 1318.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CAMERA.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAMERA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CAMERA_1.61.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/CAMERA.Rcheck' * using R version 4.4.1 (2024-06-14 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 'CAMERA/DESCRIPTION' ... OK * this is package 'CAMERA' version '1.61.0' * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'CAMERA' can be installed ... WARNING Found the following significant warnings: fastMatch.c:65:68: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] See 'F:/biocbuild/bbs-3.20-bioc/meat/CAMERA.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 8.7Mb sub-directories of 1Mb or more: mzML 2.7Mb quantiles 4.9Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'methods' 'xcms' A package should be listed in only one of these fields. * 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 'library' or 'require' call to 'methods' which was already attached by Depends. Please remove these calls from your code. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'annotateGrp' 'combineHypothese' 'fastMatch' 'naOmit' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .Call("getEIC", ..., PACKAGE = "xcms") See chapter 'System and foreign language interfaces' in the 'Writing R Extensions' manual. * checking R code for possible problems ... NOTE File 'CAMERA/R/zzz.R': .onLoad calls: require(methods) Package startup functions should not change the search path. See section 'Good practice' in '?.onAttach'. annotateGrp: no visible global function definition for 'na.omit' annotateGrpMPI2: no visible binding for global variable 'papply_commondata' cleanParallel: no visible global function definition for 'mpi.close.Rslaves' cleanParallel: no visible global function definition for 'stopCluster' compoundQuantiles: no visible global function definition for 'tail' createHypothese: no visible global function definition for 'cutree' createHypothese: no visible global function definition for 'hclust' createHypothese: no visible global function definition for 'dist' extractfragments: no visible global function definition for 'median' fast_corr: no visible global function definition for 'pt' findIsotopesForPS: no visible binding for global variable 'tableMM48' findKendrickMasses: no visible global function definition for 'rainbow' findKendrickMasses : <anonymous>: no visible global function definition for 'lines' findNeutralLoss: no visible global function definition for 'dist' findNeutralLossSpecs : <anonymous>: no visible global function definition for 'dist' fragments2metfrag : <anonymous>: no visible global function definition for 'write.table' fragments2metfusion : <anonymous>: no visible binding for global variable 'object' fragments2metfusion : <anonymous>: no visible global function definition for 'write.table' getIsotopeCluster : <anonymous>: no visible global function definition for 'na.omit' xsAnnotate: no visible global function definition for 'mpi.comm.size' xsAnnotate: no visible global function definition for 'mpi.spawn.Rslaves' xsAnnotate: no visible global function definition for 'makeCluster' xsAnnotate: no visible binding for global variable 'graphMethod' findAdducts,xsAnnotate: no visible global function definition for 'mpi.comm.size' findAdducts,xsAnnotate: no visible global function definition for 'xcmsPapply' findIsotopesWithValidation,xsAnnotate : <anonymous>: no visible global function definition for 'median' getReducedPeaklist,xsAnnotate : <anonymous> : <anonymous>: no visible global function definition for 'median' getReducedPeaklist,xsAnnotate : <anonymous>: no visible global function definition for 'prcomp' getReducedPeaklist,xsAnnotate : <anonymous>: no visible global function definition for 'na.omit' groupComplete,xsAnnotate: no visible global function definition for 'dist' groupComplete,xsAnnotate: no visible global function definition for 'cutree' groupComplete,xsAnnotate: no visible global function definition for 'hclust' groupDen,xsAnnotate: no visible global function definition for 'density' groupFWHM,xsAnnotate : <anonymous>: no visible global function definition for 'na.omit' plotEICs,xsAnnotate: no visible global function definition for 'rainbow' plotEICs,xsAnnotate: no visible global function definition for 'na.omit' plotPeakEICs,xsAnnotate : <anonymous>: no visible binding for global variable 'pc' plotPeakEICs,xsAnnotate: no visible binding for global variable 'pspec' plotPeakEICs,xsAnnotate: no visible global function definition for 'rainbow' plotPeakEICs,xsAnnotate: no visible global function definition for 'na.omit' plotPsSpectrum,xsAnnotate: no visible global function definition for 'median' plotPsSpectrum,xsAnnotate: no visible global function definition for 'na.omit' Undefined global functions or variables: cutree density dist graphMethod hclust lines makeCluster median mpi.close.Rslaves mpi.comm.size mpi.spawn.Rslaves na.omit object papply_commondata pc prcomp pspec pt rainbow stopCluster tableMM48 tail write.table xcmsPapply Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "lines") importFrom("stats", "cutree", "density", "dist", "hclust", "median", "na.omit", "prcomp", "pt") importFrom("utils", "tail", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: findKendrickMasses.Rd:21-22: Dropping empty section \details * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/CAMERA/libs/x64/CAMERA.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 groupCorr-methods 22.94 0.56 43.27 annotate-methods 6.31 0.17 26.53 getIsotopeCluster 4.22 0.09 46.09 annotateDiffreport 3.42 0.09 31.00 groupDen-methods 3.11 0.22 23.23 getPeaklist-methods 3.11 0.19 23.03 groupFWHM-methods 3.06 0.23 23.35 getReducedPeaklist-methods 3.11 0.14 23.33 findAdducts-methods 3.09 0.06 22.75 pspec2metfrag 2.80 0.11 23.47 findIsotopesWithValidation-methods 1.64 0.11 19.49 findIsotopes-methods 1.06 0.04 20.73 getpspectra 1.04 0.05 20.90 findNeutralLoss 1.05 0.01 19.76 findNeutralLossSpecs 1.03 0.03 19.33 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.R' OK * 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: 1 WARNING, 8 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/CAMERA.Rcheck/00check.log' for details.
CAMERA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CAMERA ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'CAMERA' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fastMatch.c -o fastMatch.o fastMatch.c: In function 'fastMatch': fastMatch.c:65:68: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 65 | error("fastMatch/calloc: memory could not be allocated ! (%d bytes)\n", nx * sizeof(struct idxStruct) ); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long long unsigned int | %lld gcc -shared -s -static-libgcc -o CAMERA.dll tmp.def fastMatch.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-CAMERA/00new/CAMERA/libs/x64 ** R ** data ** 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 (CAMERA)
CAMERA.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("CAMERA") || stop("unable to load CAMERA") Loading required package: CAMERA Loading required package: Biobase 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, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: xcms Loading required package: BiocParallel This is xcms version 4.3.3 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma [1] TRUE > BiocGenerics:::testPackage("CAMERA") Loading required package: xcms Loading required package: BiocParallel This is xcms version 4.3.3 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma F:/biocbuild/bbs-3.20-bioc/R/library/faahKO/cdf/WT/wt15.CDF method: bin step: 0.1 F:/biocbuild/bbs-3.20-bioc/R/library/faahKO/cdf/WT/wt16.CDF method: bin step: 0.1 F:/biocbuild/bbs-3.20-bioc/R/library/faahKO/cdf/WT/wt18.CDF method: bin step: 0.1 Loading required package: xcms Loading required package: BiocParallel This is xcms version 4.3.3 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma F:/biocbuild/bbs-3.20-bioc/R/library/faahKO/cdf/KO/ko19.CDF method: bin step: 0.1 F:/biocbuild/bbs-3.20-bioc/R/library/faahKO/cdf/KO/ko21.CDF method: bin step: 0.1 F:/biocbuild/bbs-3.20-bioc/R/library/faahKO/cdf/KO/ko22.CDF method: bin step: 0.1 Loading required package: xcms Loading required package: BiocParallel This is xcms version 4.3.3 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma F:/biocbuild/bbs-3.20-bioc/R/library/faahKO/cdf/KO/ko15.CDF method: bin step: 0.1 F:/biocbuild/bbs-3.20-bioc/R/library/faahKO/cdf/KO/ko16.CDF method: bin step: 0.1 F:/biocbuild/bbs-3.20-bioc/R/library/faahKO/cdf/KO/ko18.CDF method: bin step: 0.1 Loading required package: xcms Loading required package: BiocParallel This is xcms version 4.3.3 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma F:/biocbuild/bbs-3.20-bioc/R/library/faahKO/cdf/WT/wt19.CDF method: bin step: 0.1 F:/biocbuild/bbs-3.20-bioc/R/library/faahKO/cdf/WT/wt21.CDF method: bin step: 0.1 F:/biocbuild/bbs-3.20-bioc/R/library/faahKO/cdf/WT/wt22.CDF method: bin step: 0.1 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 321 xsAnnotate has now 321 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 321 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 229 xsAnnotate has now 229 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 229 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 244 xsAnnotate has now 244 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 244 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 321 xsAnnotate has now 321 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 321 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 321 xsAnnotate has now 321 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 321 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating isotope assignments in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 289 xsAnnotate has now 289 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 289 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 321 xsAnnotate has now 321 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 321 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 313 xsAnnotate has now 313 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 313 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 229 xsAnnotate has now 229 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 229 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 218 xsAnnotate has now 218 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 218 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 375 xsAnnotate has now 375 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 375 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 314 xsAnnotate has now 314 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 314 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 375 xsAnnotate has now 375 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 375 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 317 xsAnnotate has now 317 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 317 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 314 xsAnnotate has now 314 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 314 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 148 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 148 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 148 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 333 xsAnnotate has now 333 groups, instead of 148 Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 22 Generating peak matrix for peak annotation! Found and use user-defined ruleset! Calculating possible adducts in 333 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 254 xsAnnotate has now 254 groups, instead of 133 Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 32 Generating peak matrix for peak annotation! Found and use user-defined ruleset! Calculating possible adducts in 254 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 329 xsAnnotate has now 329 groups, instead of 133 Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 20 Generating peak matrix for peak annotation! Found and use user-defined ruleset! Calculating possible adducts in 329 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Loading required package: xcms Loading required package: BiocParallel This is xcms version 4.3.3 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 20 50 60 70 80 90 100 Found isotopes: 32 Found and use user-defined ruleset! Calculating possible adducts in 14 Groups... % finished: 20 50 60 70 80 90 100 Loading required package: xcms Loading required package: BiocParallel This is xcms version 4.3.3 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Start grouping after correlation. Calculating peak correlations in 14 Groups... % finished: 20 50 60 70 80 90 100 Calculating graph cross linking in 14 Groups... % finished: 20 50 60 70 80 90 100 New number of ps-groups: 35 xsAnnotate has now 35 groups, instead of 14 Loading required package: xcms Loading required package: BiocParallel This is xcms version 4.3.3 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Created 11 pseudospectra. Start grouping after retention time. Created 148 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 148 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 148 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 333 xsAnnotate has now 333 groups, instead of 148 Start grouping after retention time. Created 133 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of ps-groups: 329 xsAnnotate has now 329 groups, instead of 133 Start grouping after correlation. Data was not preprocessed with groupFWHM, creating one pseudospectrum with all peaks. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 1 Groups... % finished: 100 Calculating graph cross linking in 1 Groups... % finished: 100 New number of ps-groups: 316 xsAnnotate has now 316 groups, instead of 1 Start grouping after correlation. Data was not preprocessed with groupFWHM, creating one pseudospectrum with all peaks. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 1 Groups... % finished: 100 Calculating graph cross linking in 1 Groups... % finished: 100 New number of ps-groups: 316 xsAnnotate has now 316 groups, instead of 1 Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 22 Generating peak matrix for peak annotation! Found and use user-defined ruleset! Calculating possible adducts in 316 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Loading required package: xcms Loading required package: BiocParallel This is xcms version 4.3.3 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Start grouping after correlation. Data was not preprocessed with groupFWHM, creating one pseudospectrum with all peaks. Calculating peak correlations in 1 Groups... % finished: 100 Calculating graph cross linking in 1 Groups... % finished: 100 New number of ps-groups: 48 xsAnnotate has now 48 groups, instead of 1 Start grouping after correlation. Calculating peak correlations in 14 Groups... % finished: 20 50 60 70 80 90 100 Calculating graph cross linking in 14 Groups... % finished: 20 50 60 70 80 90 100 New number of ps-groups: 48 xsAnnotate has now 48 groups, instead of 14 Start grouping after correlation. Calculating peak correlations in 8 Groups... % finished: 30 60 70 80 90 100 Calculating graph cross linking in 8 Groups... % finished: 30 60 70 80 90 100 New number of ps-groups: 29 xsAnnotate has now 29 groups, instead of 14 Generating peak matrix! Run isotope peak annotation % finished: 20 50 60 70 80 90 100 Found isotopes: 32 Start grouping after correlation. Calculating peak correlations in 14 Groups... % finished: 20 50 60 70 80 90 100 Calculating graph cross linking in 14 Groups... % finished: 20 50 60 70 80 90 100 New number of ps-groups: 48 xsAnnotate has now 48 groups, instead of 14 xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 32 Found and use user-defined ruleset! Calculating possible adducts in 1 Groups... % finished: 100 Generating peak matrix! Run isotope peak annotation % finished: 20 40 50 60 70 80 90 100 Found isotopes: 23 Calculating possible adducts in 48 Groups... % finished: 20 40 50 60 70 80 90 100 Calculating possible adducts in 8 Groups... % finished: 10 Loading required package: xcms Loading required package: BiocParallel This is xcms version 4.3.3 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Loading required package: xcms Loading required package: BiocParallel This is xcms version 4.3.3 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 20 50 60 70 80 90 100 Found isotopes: 32 Calculating possible adducts in 14 Groups... % finished: 20 50 60 70 80 90 100 RUNIT TEST PROTOCOL -- Tue Aug 20 23:25:10 2024 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 0 1 Test Suite : CAMERA RUnit Tests - 20 test functions, 0 errors, 0 failures Number of test functions: 20 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 355.40 7.10 512.25
CAMERA.Rcheck/CAMERA-Ex.timings
name | user | system | elapsed | |
annotate-methods | 6.31 | 0.17 | 26.53 | |
annotateDiffreport | 3.42 | 0.09 | 31.00 | |
calcCaS-methods | 2.25 | 0.05 | 2.29 | |
cleanParallel | 0 | 0 | 0 | |
combinexsAnnos | 0 | 0 | 0 | |
compoundLibraries | 0 | 0 | 0 | |
compoundQuantiles | 0.06 | 0.02 | 0.14 | |
findAdducts-methods | 3.09 | 0.06 | 22.75 | |
findIsotopes-methods | 1.06 | 0.04 | 20.73 | |
findIsotopesWithValidation-methods | 1.64 | 0.11 | 19.49 | |
findKendrickMasses | 1.94 | 0.07 | 2.00 | |
findNeutralLoss | 1.05 | 0.01 | 19.76 | |
findNeutralLossSpecs | 1.03 | 0.03 | 19.33 | |
getAllPeakEICs-methods | 4.36 | 0.19 | 4.55 | |
getAtomCount-compoundQuantiles-method | 0.08 | 0.00 | 0.10 | |
getIsotopeCluster | 4.22 | 0.09 | 46.09 | |
getIsotopeProportion-compoundQuantiles-method | 0.06 | 0.01 | 0.11 | |
getPeaklist-methods | 3.11 | 0.19 | 23.03 | |
getReducedPeaklist-methods | 3.11 | 0.14 | 23.33 | |
getpspectra | 1.04 | 0.05 | 20.90 | |
groupCorr-methods | 22.94 | 0.56 | 43.27 | |
groupDen-methods | 3.11 | 0.22 | 23.23 | |
groupFWHM-methods | 3.06 | 0.23 | 23.35 | |
massWindowSizes | 0 | 0 | 0 | |
pspec2metfrag | 2.80 | 0.11 | 23.47 | |
ruleSet-class | 0.05 | 0.02 | 0.06 | |
xsAnnotate | 1.97 | 0.08 | 2.04 | |