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This page was generated on 2021-10-15 15:06:29 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the Biobase package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 154/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Biobase 2.52.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Biobase |
| Version: 2.52.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Biobase.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Biobase_2.52.0.tar.gz |
| StartedAt: 2021-10-14 16:41:53 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 16:43:40 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 107.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Biobase.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Biobase.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Biobase_2.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Biobase.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Biobase/DESCRIPTION’ ... OK * this is package ‘Biobase’ version ‘2.52.0’ * 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: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Biobase’ can be installed ... OK * 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 ... 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/Biobase.Rcheck/00check.log’ for details.
Biobase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Biobase ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘Biobase’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Rinit.c -o Rinit.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c anyMissing.c -o anyMissing.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c envir.c -o envir.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c matchpt.c -o matchpt.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c rowMedians.c -o rowMedians.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c sublist_extract.c -o sublist_extract.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
RUNIT TEST PROTOCOL -- Thu Oct 14 16:43:02 2021
***********************************************
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
15.233 0.257 15.511
Biobase.Rcheck/tests/test-rowMedians.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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
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(): 0.176
Random test #2
rowMedians()/apply(): 0.183
rowMedians()/rowMedians2(): 0.413
Random test #3
rowMedians()/apply(): 0.0313
Random test #4
rowMedians()/apply(): 0.126
rowMedians()/rowMedians2(): 0.25
Random test #5
rowMedians()/apply(): 0.257
rowMedians()/rowMedians2(): 0.427
Random test #6
rowMedians()/apply(): 0.21
rowMedians()/rowMedians2(): 0.395
Random test #7
rowMedians()/apply(): 0.221
Random test #8
rowMedians()/apply(): 0.00775
rowMedians()/rowMedians2(): Inf
Random test #9
rowMedians()/apply(): 0.2
Random test #10
rowMedians()/apply(): 0.0593
Random test #11
rowMedians()/apply(): 0.093
Random test #12
rowMedians()/apply(): 0.0851
Random test #13
rowMedians()/apply(): 0.233
rowMedians()/rowMedians2(): 0.875
Random test #14
rowMedians()/apply(): 0.176
Random test #15
rowMedians()/apply(): 0.245
Random test #16
rowMedians()/apply(): 0.11
rowMedians()/rowMedians2(): 0.34
Random test #17
rowMedians()/apply(): 0.191
Random test #18
rowMedians()/apply(): 0.136
rowMedians()/rowMedians2(): 0.696
Random test #19
rowMedians()/apply(): 0.371
rowMedians()/rowMedians2(): 0.92
Random test #20
rowMedians()/apply(): 0.225
rowMedians()/rowMedians2(): 0.339
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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 587513 31.4 1162404 62.1 NA 1042371 55.7
Vcells 2069780 15.8 12255594 93.6 65536 12295273 93.9
> 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 587529 31.4 1162404 62.1 NA 1162404 62.1
Vcells 2070797 15.8 12255594 93.6 65536 12295273 93.9
> 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 587529 31.4 1162404 62.1 NA 1162404 62.1
Vcells 2069922 15.8 12255594 93.6 65536 12295273 93.9
> stopifnot(all.equal(y0,y1))
> cat(sprintf("rowMedians()/apply(): %.3g\n", (t1/t0)[3]))
rowMedians()/apply(): 0.175
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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
22.134 0.763 22.896
Biobase.Rcheck/Biobase-Ex.timings
| name | user | system | elapsed | |
| Aggregate | 0.006 | 0.001 | 0.006 | |
| ScalarObject-class | 0.055 | 0.001 | 0.056 | |
| addVig2Menu | 0 | 0 | 0 | |
| anyMissing | 0.002 | 0.000 | 0.002 | |
| cache | 0.002 | 0.001 | 0.003 | |
| channel | 0.176 | 0.017 | 0.194 | |
| channelNames | 0.043 | 0.000 | 0.043 | |
| class.AnnotatedDataFrame | 0.026 | 0.002 | 0.028 | |
| class.ExpressionSet | 0.175 | 0.005 | 0.179 | |
| class.MIAxE | 0.018 | 0.001 | 0.018 | |
| class.MultiSet | 0.025 | 0.000 | 0.026 | |
| class.NChannelSet | 0.168 | 0.003 | 0.170 | |
| class.Versioned | 0.077 | 0.002 | 0.079 | |
| class.VersionedBiobase | 0.031 | 0.001 | 0.033 | |
| class.Versions | 0.011 | 0.001 | 0.012 | |
| class.VersionsNull | 0.001 | 0.001 | 0.002 | |
| class.container | 0.004 | 0.000 | 0.004 | |
| class.eSet | 0.073 | 0.002 | 0.075 | |
| classVersion | 0.003 | 0.001 | 0.004 | |
| contents | 0.000 | 0.001 | 0.002 | |
| copyEnv | 0 | 0 | 0 | |
| copySubstitute | 0.010 | 0.006 | 0.017 | |
| createPackage | 0.006 | 0.003 | 0.010 | |
| data.aaMap | 0.002 | 0.002 | 0.003 | |
| data.geneData | 0.031 | 0.005 | 0.036 | |
| data.reporter | 0.001 | 0.001 | 0.003 | |
| data.sample.ExpressionSet | 0.016 | 0.002 | 0.018 | |
| data.sample.MultiSet | 0.006 | 0.001 | 0.008 | |
| dumpPackTxt | 0.001 | 0.001 | 0.002 | |
| esApply | 1.602 | 0.016 | 1.624 | |
| getPkgVigs | 0.010 | 0.003 | 0.015 | |
| isCurrent | 0.034 | 0.002 | 0.035 | |
| isUnique | 0.001 | 0.000 | 0.001 | |
| isVersioned | 0.013 | 0.000 | 0.013 | |
| lcSuffix | 0.001 | 0.001 | 0.003 | |
| listLen | 0.001 | 0.000 | 0.002 | |
| makeDataPackage | 0.068 | 0.006 | 0.075 | |
| matchpt | 0.004 | 0.001 | 0.005 | |
| multiassign | 0.000 | 0.001 | 0.001 | |
| note | 0 | 0 | 0 | |
| openPDF | 0 | 0 | 0 | |
| openVignette | 0 | 0 | 0 | |
| package.version | 0.001 | 0.001 | 0.001 | |
| read.AnnotatedDataFrame | 0.021 | 0.002 | 0.023 | |
| read.MIAME | 0.002 | 0.000 | 0.003 | |
| readExpressionSet | 0.062 | 0.003 | 0.066 | |
| reverseSplit | 0.001 | 0.001 | 0.001 | |
| rowMedians | 0.046 | 0.006 | 0.052 | |
| rowQ | 0.021 | 0.012 | 0.033 | |
| selectChannels | 0.061 | 0.001 | 0.062 | |
| selectSome | 0.000 | 0.000 | 0.001 | |
| strbreak | 0.001 | 0.000 | 0.002 | |
| subListExtract | 0.921 | 0.030 | 0.953 | |
| testBioCConnection | 0.005 | 0.003 | 0.538 | |
| updateOldESet | 0.000 | 0.001 | 0.000 | |
| validMsg | 0.001 | 0.000 | 0.000 | |