Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 172/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Biobase 2.66.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the Biobase package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Biobase.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: Biobase |
Version: 2.66.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Biobase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Biobase_2.66.0.tar.gz |
StartedAt: 2024-12-20 00:11:41 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:14:30 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 169.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Biobase.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Biobase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Biobase_2.66.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Biobase.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Biobase/DESCRIPTION’ ... OK * this is package ‘Biobase’ version ‘2.66.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Biobase’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... OK * 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 ... OK * 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 compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.R’ Running ‘test-rowMedians.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 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Biobase.Rcheck/00check.log’ for details.
Biobase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Biobase ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘Biobase’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rinit.c -o Rinit.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c anyMissing.c -o anyMissing.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c envir.c -o envir.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matchpt.c -o matchpt.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowMedians.c -o rowMedians.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sublist_extract.c -o sublist_extract.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-Biobase/00new/Biobase/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 (Biobase)
Biobase.Rcheck/tests/test-all.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > BiocGenerics:::testPackage("Biobase") 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, saveRDS, 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")'. RUNIT TEST PROTOCOL -- Fri Dec 20 00:13:33 2024 *********************************************** Number of test functions: 101 Number of errors: 0 Number of failures: 0 1 Test Suite : Biobase RUnit Tests - 101 test functions, 0 errors, 0 failures Number of test functions: 101 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 23.968 0.424 26.289
Biobase.Rcheck/tests/test-rowMedians.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > library(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, saveRDS, 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")'. > set.seed(1) > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Consistency checks > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > > # rowMedians() by rowQ() > rowMedians2 <- function(imat) { + nr <- ncol(imat) + half <- (nr + 1)/2 + if (nr%%2 == 1) { + return(rowQ(imat, half)) + } else { + return((rowQ(imat, half) + rowQ(imat, half+1))/2) + } + } > > cat("Consistency checks:\n") Consistency checks: > set.seed(1) > for (kk in 1:20) { + cat("Random test #", kk, "\n", sep="") + + # Simulate data in a matrix of any shape + nrow <- sample(2000, size=1) + ncol <- sample(2000, size=1) + x <- rnorm(nrow*ncol) + dim(x) <- c(nrow, ncol) + + # Add NAs? + nas <- sample(c(TRUE,FALSE), size=1) + if (nas) { + nna <- sample(nrow*ncol, size=1) + x[sample(length(x), size=nna)] <- NA + } + + na.rm <- nas + t1 <- system.time({ + y1 <- rowMedians(x, na.rm=na.rm) + }) + t2 <- system.time({ + y2 <- apply(x, MARGIN=1, FUN=median, na.rm=na.rm) + }) + # When all values of 'y2' are NA, 'y2' is logical + if (is.logical(y2)) y2 <- as.double(y2) + stopifnot(all.equal(y1,y2)) + cat(sprintf("rowMedians()/apply(): %.3g\n", (t1/t2)[3])) + + if (!nas) { + t3 <- system.time({ + y3 <- rowMedians2(x) + }) + stopifnot(all.equal(y1,y3)) + cat(sprintf("rowMedians()/rowMedians2(): %.3g\n", (t1/t3)[3])) + } + } Random test #1 rowMedians()/apply(): 0.182 Random test #2 rowMedians()/apply(): 0.0912 rowMedians()/rowMedians2(): 0.382 Random test #3 rowMedians()/apply(): 0.02 Random test #4 rowMedians()/apply(): 0.124 rowMedians()/rowMedians2(): 0.278 Random test #5 rowMedians()/apply(): 0.204 rowMedians()/rowMedians2(): 0.404 Random test #6 rowMedians()/apply(): 0.188 rowMedians()/rowMedians2(): 0.361 Random test #7 rowMedians()/apply(): 0.241 Random test #8 rowMedians()/apply(): 0 rowMedians()/rowMedians2(): 0 Random test #9 rowMedians()/apply(): 0.1 Random test #10 rowMedians()/apply(): 0.0522 Random test #11 rowMedians()/apply(): 0.098 Random test #12 rowMedians()/apply(): 0.102 Random test #13 rowMedians()/apply(): 0.212 rowMedians()/rowMedians2(): 0.778 Random test #14 rowMedians()/apply(): 0.158 Random test #15 rowMedians()/apply(): 0.171 Random test #16 rowMedians()/apply(): 0.107 rowMedians()/rowMedians2(): 0.433 Random test #17 rowMedians()/apply(): 0.166 Random test #18 rowMedians()/apply(): 0.0649 rowMedians()/rowMedians2(): 0.652 Random test #19 rowMedians()/apply(): 0.259 rowMedians()/rowMedians2(): 0.75 Random test #20 rowMedians()/apply(): 0.227 rowMedians()/rowMedians2(): 0.402 > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Benchmarking > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > cat("Benchmarking:\n") Benchmarking: > > # Simulate data in a matrix of any shape > nrow <- 1000 > ncol <- 1000 > x <- rnorm(nrow*ncol) > dim(x) <- c(nrow, ncol) > > gc() used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) Ncells 599764 32.1 1201512 64.2 NA 1063438 56.8 Vcells 2098986 16.1 12255594 93.6 65536 12334539 94.2 > t0 <- system.time({ + for (rr in 1:20) + y0 <- apply(x, MARGIN=1, FUN=median, na.rm=FALSE) + }) > gc() used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) Ncells 599780 32.1 1201512 64.2 NA 1201512 64.2 Vcells 2100003 16.1 12255594 93.6 65536 12334539 94.2 > t1 <- system.time({ + for (rr in 1:20) + y1 <- rowMedians(x, na.rm=FALSE) + }) > gc() used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) Ncells 599780 32.1 1201512 64.2 NA 1201512 64.2 Vcells 2099128 16.1 12255594 93.6 65536 12334539 94.2 > stopifnot(all.equal(y0,y1)) > cat(sprintf("rowMedians()/apply(): %.3g\n", (t1/t0)[3])) rowMedians()/apply(): 0.148 > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Consistency checks > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > cat("Consistency checks without NAs:\n") Consistency checks without NAs: > for (kk in 1:20) { + cat("Random test #", kk, "\n", sep="") + + # Simulate data in a matrix of any shape + nrow <- sample(1000, size=1) + ncol <- sample(1000, size=1) + x <- rnorm(nrow*ncol) + dim(x) <- c(nrow, ncol) + + t0 <- system.time({ + y0 <- apply(x, MARGIN=1, FUN=median, na.rm=FALSE) + }) + t1 <- system.time({ + y1 <- rowMedians(x, na.rm=FALSE) + }) + stopifnot(all.equal(y0,y1)) + } # for (kk in ...) Random test #1 Random test #2 Random test #3 Random test #4 Random test #5 Random test #6 Random test #7 Random test #8 Random test #9 Random test #10 Random test #11 Random test #12 Random test #13 Random test #14 Random test #15 Random test #16 Random test #17 Random test #18 Random test #19 Random test #20 > > > > cat("Consistency checks with NAs:\n") Consistency checks with NAs: > for (kk in 1:20) { + cat("Random test #", kk, "\n", sep="") + + # Simulate data in a matrix of any shape + nrow <- sample(1000, size=1) + ncol <- sample(1000, size=1) + x <- rnorm(nrow*ncol) + dim(x) <- c(nrow, ncol) + + # Add NAs + nna <- sample(nrow*ncol-1, size=1) + x[sample(length(x), size=nna)] <- NA + + t0 <- system.time({ + y0 <- apply(x, MARGIN=1, FUN=median, na.rm=TRUE) + y0[is.na(y0)] <- NA + }) + t1 <- system.time({ + y1 <- rowMedians(x, na.rm=TRUE) + }) + stopifnot(all.equal(y0,y1)) + } # for (kk in ...) Random test #1 Random test #2 Random test #3 Random test #4 Random test #5 Random test #6 Random test #7 Random test #8 Random test #9 Random test #10 Random test #11 Random test #12 Random test #13 Random test #14 Random test #15 Random test #16 Random test #17 Random test #18 Random test #19 Random test #20 > > proc.time() user system elapsed 28.237 0.898 30.882
Biobase.Rcheck/Biobase-Ex.timings
name | user | system | elapsed | |
Aggregate | 0.010 | 0.001 | 0.012 | |
ScalarObject-class | 0.018 | 0.001 | 0.020 | |
addVig2Menu | 0.000 | 0.000 | 0.001 | |
anyMissing | 0.002 | 0.001 | 0.002 | |
cache | 0.004 | 0.002 | 0.006 | |
channel | 0.363 | 0.034 | 0.418 | |
channelNames | 0.086 | 0.002 | 0.092 | |
class.AnnotatedDataFrame | 0.053 | 0.003 | 0.057 | |
class.ExpressionSet | 0.366 | 0.016 | 0.439 | |
class.MIAxE | 0.030 | 0.002 | 0.032 | |
class.MultiSet | 0.051 | 0.001 | 0.053 | |
class.NChannelSet | 0.273 | 0.005 | 0.280 | |
class.Versioned | 0.105 | 0.004 | 0.112 | |
class.VersionedBiobase | 0.049 | 0.002 | 0.052 | |
class.Versions | 0.020 | 0.001 | 0.021 | |
class.VersionsNull | 0.001 | 0.000 | 0.002 | |
class.container | 0.004 | 0.001 | 0.006 | |
class.eSet | 0.152 | 0.004 | 0.168 | |
classVersion | 0.007 | 0.001 | 0.008 | |
contents | 0.001 | 0.002 | 0.003 | |
copyEnv | 0.001 | 0.000 | 0.001 | |
copySubstitute | 0.016 | 0.015 | 0.034 | |
createPackage | 0.008 | 0.006 | 0.015 | |
data.aaMap | 0.002 | 0.002 | 0.004 | |
data.geneData | 0.034 | 0.008 | 0.042 | |
data.reporter | 0.002 | 0.002 | 0.004 | |
data.sample.ExpressionSet | 0.018 | 0.003 | 0.023 | |
data.sample.MultiSet | 0.007 | 0.002 | 0.009 | |
dumpPackTxt | 0.001 | 0.002 | 0.004 | |
esApply | 2.458 | 0.020 | 2.650 | |
getPkgVigs | 0.013 | 0.005 | 0.021 | |
isCurrent | 0.054 | 0.003 | 0.057 | |
isUnique | 0.001 | 0.001 | 0.002 | |
isVersioned | 0.023 | 0.001 | 0.025 | |
lcSuffix | 0.003 | 0.001 | 0.003 | |
listLen | 0.001 | 0.000 | 0.001 | |
makeDataPackage | 0.091 | 0.009 | 0.103 | |
matchpt | 0.008 | 0.001 | 0.009 | |
multiassign | 0.001 | 0.001 | 0.001 | |
note | 0.001 | 0.001 | 0.001 | |
openPDF | 0.001 | 0.000 | 0.001 | |
openVignette | 0.000 | 0.000 | 0.001 | |
package.version | 0.001 | 0.001 | 0.003 | |
read.AnnotatedDataFrame | 0.018 | 0.003 | 0.021 | |
read.MIAME | 0.003 | 0.001 | 0.004 | |
readExpressionSet | 0.096 | 0.003 | 0.102 | |
reverseSplit | 0.001 | 0.001 | 0.002 | |
rowMedians | 0.062 | 0.007 | 0.069 | |
rowQ | 0.025 | 0.019 | 0.044 | |
selectChannels | 0.084 | 0.001 | 0.089 | |
selectSome | 0.000 | 0.000 | 0.001 | |
strbreak | 0.002 | 0.001 | 0.002 | |
subListExtract | 1.309 | 0.042 | 1.372 | |
testBioCConnection | 0.027 | 0.011 | 3.460 | |
updateOldESet | 0.000 | 0.000 | 0.001 | |
validMsg | 0.000 | 0.000 | 0.001 | |