Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-30 12:07 -0400 (Tue, 30 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4843 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4631 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4575 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 1631/2337 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pRoloc 1.49.1 (landing page) Lisa Breckels
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the pRoloc package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pRoloc.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: pRoloc |
Version: 1.49.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:pRoloc.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings pRoloc_1.49.1.tar.gz |
StartedAt: 2025-09-30 11:35:35 -0000 (Tue, 30 Sep 2025) |
EndedAt: 2025-09-30 11:52:42 -0000 (Tue, 30 Sep 2025) |
EllapsedTime: 1027.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: pRoloc.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:pRoloc.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings pRoloc_1.49.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/pRoloc.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pRoloc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pRoloc’ version ‘1.49.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 28 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘pRoloc’ can be installed ... OK * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking installed package size ... INFO installed size is 5.1Mb sub-directories of 1Mb or more: R 1.2Mb libs 2.4Mb * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE ':::' calls which should be '::': ‘MLInterfaces:::.macroF1’ ‘MLInterfaces:::.precision’ ‘MLInterfaces:::.recall’ ‘MLInterfaces:::es2df’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘MSnbase:::.sameNbCol’ ‘MSnbase:::getVariableName’ ‘MSnbase:::logging’ ‘MSnbase:::nologging’ ‘caret:::predict.plsda’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘getAttributesOfInterest0’ ‘getAttributesOfInterestX’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... WARNING checkRd: (7) plsdaOptimisation.Rd:66-81: Tag \donttest not recognized * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'AnnotationParams-class.Rd': ‘getGOFromFeatures’ ‘makeGoSet’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: AnnotationParams-class.Rd: getGOFromFeatures, makeGoSet GenRegRes-class.Rd: MSnSet-class MLearn-methods.Rd: MSnSet-class, xvalSpec, MLearn QSep-class.Rd: MSnSet-class, Versioned-class SpatProtVis-class.Rd: MSnSet-class clustDist.Rd: MSnSet-class getMarkerClasses.Rd: MSnSet-class getMarkers.Rd: MSnSet-class getPredictions.Rd: MSnSet-class highlightOnPlot.Rd: FeaturesOfInterest-class knnClassification.Rd: MSnSet-class, knn knnOptimisation.Rd: MSnSet-class, knn knntlClassification.Rd: MSnSet-class knntlOptimisation.Rd: MSnSet-class ksvmClassification.Rd: MSnSet-class, ksvm ksvmOptimisation.Rd: MSnSet-class, ksvm minMarkers.Rd: MSnSet-class move2Ds.Rd: MSnSetList nbClassification.Rd: MSnSet-class, naiveBayes nbOptimisation.Rd: MSnSet-class, naiveBayes nnetClassification.Rd: MSnSet-class, nnet nnetOptimisation.Rd: MSnSet-class, nnet orgQuants.Rd: MSnSet-class perTurboClassification.Rd: MSnSet-class, ginv perTurboOptimisation.Rd: MSnSet-class, ginv phenoDisco.Rd: filterNA plot2Ds.Rd: MSnSet-class, MSnSetList plsdaClassification.Rd: MSnSet-class, plsda plsdaOptimisation.Rd: MSnSet-class, plsda rfClassification.Rd: MSnSet-class, randomForest rfOptimisation.Rd: MSnSet-class, randomForest sampleMSnSet.Rd: MSnSet-class svmClassification.Rd: MSnSet-class, svm svmOptimisation.Rd: MSnSet-class, svm testMSnSet.Rd: MSnSet-class testMarkers.Rd: MSnSet-class 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: ‘addGoAnnotations’ ‘flipGoTermId’ ‘getGOEvidenceCodes’ ‘getGOFromFeatures’ ‘goIdToTerm’ ‘goTermToId’ ‘makeGoSet’ ‘prettyGoTermId’ ‘showGOEvidenceCodes’ Undocumented data sets: ‘andy2011params’ ‘dunkley2006params’ All user-level objects in a package 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 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 compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed knntlClassification 22.403 1.369 26.729 knntlOptimisation 17.959 1.356 26.506 perTurboClassification 16.589 0.190 24.475 perTurboOptimisation 16.403 0.183 21.921 plot2D 9.546 0.143 12.015 rfClassification 8.126 0.311 14.868 nnetClassification 8.073 0.120 9.203 nnetOptimisation 8.020 0.143 10.437 svmOptimisation 7.594 0.011 11.251 svmClassification 7.369 0.099 8.816 rfOptimisation 7.039 0.003 10.005 SpatProtVis-class 6.581 0.409 8.649 ksvmClassification 6.402 0.203 7.414 ksvmOptimisation 4.940 0.093 7.381 move2Ds 2.860 0.092 5.812 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 3 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/pRoloc.Rcheck/00check.log’ for details.
pRoloc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL pRoloc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘pRoloc’ ... ** this is package ‘pRoloc’ version ‘1.49.1’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c dmvtCpp.cpp -o dmvtCpp.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c pRoloc.cpp -o pRoloc.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o pRoloc.so RcppExports.o dmvtCpp.o pRoloc.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-pRoloc/00new/pRoloc/libs ** 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 ** 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 (pRoloc)
pRoloc.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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. > > # The setting of R_TESTS exists to work around an R bug. See > # https://github.com/hadley/testthat/issues/144 > # We should remove it when the issue is resolved. > Sys.setenv("R_TESTS" = "") > > library("testthat") > library("pRoloc") Loading required package: MSnbase Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 object is masked from 'package:utils': findMatches 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 2.35.2 Visit https://lgatto.github.io/MSnbase/ to get started. Consider switching to the 'R for Mass Spectrometry' packages - see https://RforMassSpectrometry.org for details. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws Loading required package: MLInterfaces Loading required package: annotate Loading required package: AnnotationDbi Loading required package: IRanges Loading required package: XML Attaching package: 'annotate' The following object is masked from 'package:mzR': nChrom Loading required package: cluster Loading required package: BiocParallel This is pRoloc version 1.49.1 Visit https://lgatto.github.io/pRoloc/ to get started. > library("pRolocdata") This is pRolocdata version 1.47.0. Use 'pRolocdata()' to list available data sets. > > test_check("pRoloc") Object of class "SpatProtVis" Data: dunkley2006 Visualisation methods: PCA, MDS, kpca Done. organelleMarkers ORG1 ORG2 ORG3 ORG4 ORG5 3 2 3 1 1 organelleMarkers ORG1 ORG2 ORG3 ORG4 ORG5 5 2 1 1 1 organelleMarkers ORG1 unknown 3 7 organelleMarkers ORG1 unknown 2 8 [1] "markers" [1] "xx" [1] "markers" [1] "xx" [1] "markers" [1] "xx" [1] "markers" # weights: 269 initial value 666.839513 iter 10 value 207.573433 iter 20 value 34.513121 iter 30 value 1.438035 iter 40 value 0.496168 iter 50 value 0.419018 iter 60 value 0.386372 iter 70 value 0.360129 iter 80 value 0.324298 iter 90 value 0.294123 iter 100 value 0.252996 final value 0.252996 stopped after 100 iterations [1] "xx" # weights: 269 initial value 666.839513 iter 10 value 207.573433 iter 20 value 34.513121 iter 30 value 1.438035 iter 40 value 0.496168 iter 50 value 0.419018 iter 60 value 0.386372 iter 70 value 0.360129 iter 80 value 0.324298 iter 90 value 0.294123 iter 100 value 0.252996 final value 0.252996 stopped after 100 iterations [1] "markers" [1] "xx" [1] "pd.markers" Common markers: 0 Unique x markers: 49 Unique y markers: 34 Common unkowns: 11 Unique x unknowns: 40 Unique y unknowns: 66 my mx ER lumen ER membrane Golgi Mitochondrion PM Plastid Ribosome ER lumen 14 0 0 0 0 0 0 ER membrane 0 45 0 0 0 0 0 Golgi 0 0 28 0 0 0 0 Mitochondrion 0 0 0 55 0 0 0 PM 0 0 0 0 46 0 0 Plastid 0 0 0 0 0 20 0 Ribosome 0 0 0 0 0 0 19 TGN 0 0 0 0 0 0 0 unknown 0 0 0 0 0 0 0 vacuole 0 0 0 0 0 0 0 my mx TGN unknown vacuole ER lumen 0 0 0 ER membrane 0 0 0 Golgi 0 0 0 Mitochondrion 0 0 0 PM 0 0 0 Plastid 0 0 0 Ribosome 0 0 0 TGN 13 0 0 unknown 0 428 0 vacuole 0 0 21 [ FAIL 0 | WARN 2 | SKIP 0 | PASS 119 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 119 ] > > proc.time() user system elapsed 99.250 2.219 129.116
pRoloc.Rcheck/pRoloc-Ex.timings
name | user | system | elapsed | |
AnnotationParams-class | 0 | 0 | 0 | |
ClustDist-class | 0.844 | 0.036 | 1.049 | |
ClustDistList-class | 0.314 | 0.056 | 0.569 | |
GenRegRes-class | 0.001 | 0.000 | 0.006 | |
QSep-class | 0.521 | 0.021 | 1.033 | |
SpatProtVis-class | 6.581 | 0.409 | 8.649 | |
addLegend | 0.257 | 0.008 | 0.266 | |
addMarkers | 0.251 | 0.008 | 0.486 | |
checkFeatureNamesOverlap | 0.517 | 0.017 | 1.068 | |
checkFvarOverlap | 0.045 | 0.000 | 0.088 | |
chi2-methods | 0.005 | 0.000 | 0.010 | |
classWeights | 0.139 | 0.005 | 0.297 | |
clustDist | 0.506 | 0.012 | 0.591 | |
empPvalues | 0.105 | 0.007 | 0.115 | |
fDataToUnknown | 0.064 | 0.000 | 0.064 | |
filterBinMSnSet | 0.244 | 0.019 | 0.265 | |
filterMinMarkers | 0.101 | 0.008 | 0.109 | |
filterZeroCols | 0.122 | 0.011 | 0.135 | |
getMarkerClasses | 0.051 | 0.000 | 0.052 | |
getMarkers | 0.049 | 0.008 | 0.058 | |
getNormDist | 0.517 | 0.020 | 0.609 | |
getPredictions | 0.398 | 0.036 | 0.436 | |
getStockcol | 0.140 | 0.008 | 0.148 | |
highlightOnPlot | 0.632 | 0.015 | 0.787 | |
knnClassification | 1.632 | 0.020 | 1.743 | |
knnOptimisation | 1.570 | 0.032 | 1.605 | |
knntlClassification | 22.403 | 1.369 | 26.729 | |
knntlOptimisation | 17.959 | 1.356 | 26.506 | |
ksvmClassification | 6.402 | 0.203 | 7.414 | |
ksvmOptimisation | 4.940 | 0.093 | 7.381 | |
markerMSnSet | 0.372 | 0.004 | 0.750 | |
markers | 0.087 | 0.004 | 0.184 | |
minMarkers | 0.058 | 0.005 | 0.125 | |
mixing_posterior_check | 0 | 0 | 0 | |
move2Ds | 2.860 | 0.092 | 5.812 | |
mrkConsProfiles | 0.325 | 0.004 | 0.662 | |
mrkHClust | 0.101 | 0.004 | 0.210 | |
nbClassification | 3.491 | 0.092 | 4.970 | |
nbOptimisation | 3.442 | 0.044 | 4.696 | |
nicheMeans2D | 0 | 0 | 0 | |
nndist-methods | 0.270 | 0.009 | 0.562 | |
nnetClassification | 8.073 | 0.120 | 9.203 | |
nnetOptimisation | 8.020 | 0.143 | 10.437 | |
orgQuants | 0.272 | 0.023 | 0.299 | |
pRolocmarkers | 0.036 | 0.001 | 0.100 | |
perTurboClassification | 16.589 | 0.190 | 24.475 | |
perTurboOptimisation | 16.403 | 0.183 | 21.921 | |
phenoDisco | 0 | 0 | 0 | |
plot2D | 9.546 | 0.143 | 12.015 | |
plot2Ds | 0.545 | 0.016 | 0.899 | |
plotConsProfiles | 0.531 | 0.012 | 0.568 | |
plotDist | 0.208 | 0.001 | 0.209 | |
plsdaClassification | 0 | 0 | 0 | |
rfClassification | 8.126 | 0.311 | 14.868 | |
rfOptimisation | 7.039 | 0.003 | 10.005 | |
sampleMSnSet | 0.076 | 0.006 | 0.082 | |
spatial2D | 0.000 | 0.000 | 0.001 | |
svmClassification | 7.369 | 0.099 | 8.816 | |
svmOptimisation | 7.594 | 0.011 | 11.251 | |
tagm-map | 1.445 | 0.028 | 1.874 | |
testMSnSet | 0.320 | 0.004 | 0.327 | |
testMarkers | 0.037 | 0.000 | 0.040 | |
thetas | 0.007 | 0.000 | 0.007 | |
zerosInBinMSnSet | 1.831 | 0.023 | 2.187 | |