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This page was generated on 2026-05-20 14:26 -0400 (Wed, 20 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 (2026-04-24) -- "Because it was There" 918
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Package 25/229HostnameOS / ArchINSTALLBUILDCHECKBIOCCHECK
Biobase 2.73.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2026-05-20 12:00 -0400 (Wed, 20 May 2026)
git_url: https://git.bioconductor.org/packages/Biobase
git_branch: devel
git_last_commit: c1f775a
git_last_commit_date: 2026-04-28 18:51:49 -0400 (Tue, 28 Apr 2026)
teran2Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    OK    ERRORS  

CHECK results for Biobase on teran2

To the developers/maintainers of the Biobase package:
- 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.

raw results


Summary

Package: Biobase
Version: 2.73.1
Command: /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/R CMD check --install=check:Biobase.install-out.txt --library=/home/rapidbuild/bbs-3.24-bioc-rapid/R/site-library --timings Biobase_2.73.1.tar.gz
StartedAt: 2026-05-20 12:55:21 -0400 (Wed, 20 May 2026)
EndedAt: 2026-05-20 12:56:15 -0400 (Wed, 20 May 2026)
EllapsedTime: 54.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Biobase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/R CMD check --install=check:Biobase.install-out.txt --library=/home/rapidbuild/bbs-3.24-bioc-rapid/R/site-library --timings Biobase_2.73.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/Biobase.Rcheck’
* using R version 4.6.0 (2026-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-20 16:55:21 UTC
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.73.1’
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  class.AnnotatedDataFrame.Rd: updateObject
  class.ExpressionSet.Rd: updateObject
  class.MIAME.Rd: updateObject
  class.MultiSet.Rd: updateObject
  class.NChannelSet.Rd: updateObject
  class.SnpSet.Rd: updateObject
  class.eSet.Rd: updateObject
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/Biobase.Rcheck/00check.log’
for details.

Installation output

Biobase.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/R CMD INSTALL Biobase
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library’
* installing *source* package ‘Biobase’ ...
** this is package ‘Biobase’ version ‘2.73.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Rinit.c -o Rinit.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c envir.c -o envir.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c matchpt.c -o matchpt.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c rowMedians.c -o rowMedians.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu2x -shared -L/usr/local/lib -o Biobase.so Rinit.o envir.o matchpt.o rowMedians.o sublist_extract.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-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)

Tests output

Biobase.Rcheck/tests/test-all.Rout


R version 4.6.0 (2026-04-24) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> BiocGenerics:::testPackage("Biobase")

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.



RUNIT TEST PROTOCOL -- Wed May 20 12:55:51 2026 
*********************************************** 
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 
Warning message:
In environment(FUN) <- e1 :
  setting environment(<primitive function>) is not possible and trying it is deprecated
> 
> proc.time()
   user  system elapsed 
  6.128   0.118   6.276

Biobase.Rcheck/tests/test-rowMedians.Rout


R version 4.6.0 (2026-04-24) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> library(Biobase)
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

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(): 0.368
Random test #2
rowMedians()/apply(): 0.185
rowMedians()/rowMedians2(): 0.343
Random test #3
rowMedians()/apply(): 0.111
Random test #4
rowMedians()/apply(): 0.281
rowMedians()/rowMedians2(): 0.333
Random test #5
rowMedians()/apply(): 0.356
rowMedians()/rowMedians2(): 0.425
Random test #6
rowMedians()/apply(): 0.4
rowMedians()/rowMedians2(): 0.414
Random test #7
rowMedians()/apply(): 0.416
Random test #8
rowMedians()/apply(): 0
rowMedians()/rowMedians2(): NaN
Random test #9
rowMedians()/apply(): 0.4
Random test #10
rowMedians()/apply(): 0.0833
Random test #11
rowMedians()/apply(): 0.273
Random test #12
rowMedians()/apply(): 0.208
Random test #13
rowMedians()/apply(): 0.4
rowMedians()/rowMedians2(): 0.8
Random test #14
rowMedians()/apply(): 0.333
Random test #15
rowMedians()/apply(): 0.328
Random test #16
rowMedians()/apply(): 0.216
rowMedians()/rowMedians2(): 0.355
Random test #17
rowMedians()/apply(): 0.271
Random test #18
rowMedians()/apply(): 0.2
rowMedians()/rowMedians2(): 0.769
Random test #19
rowMedians()/apply(): 0.508
rowMedians()/rowMedians2(): 0.857
Random test #20
rowMedians()/apply(): 0.361
rowMedians()/rowMedians2(): 0.452
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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) max used (Mb)
Ncells  605661 32.4    1216545 65.0  1112163 59.4
Vcells 2109385 16.1   12255594 93.6 12344482 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) max used (Mb)
Ncells  605677 32.4    1216545 65.0  1216545 65.0
Vcells 2110402 16.2   12255594 93.6 12344482 94.2
> t1 <- system.time({
+   for (rr in 1:20)
+     y1 <- rowMedians(x, na.rm=FALSE)
+ })
> gc()
          used (Mb) gc trigger (Mb) max used (Mb)
Ncells  605677 32.4    1216545 65.0  1216545 65.0
Vcells 2109527 16.1   12255594 93.6 12344482 94.2
> stopifnot(all.equal(y0,y1))
> cat(sprintf("rowMedians()/apply(): %.3g\n", (t1/t0)[3]))
rowMedians()/apply(): 0.291
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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 
 11.242   0.232  11.463

Example timings

Biobase.Rcheck/Biobase-Ex.timings

nameusersystemelapsed
Aggregate0.0030.0000.003
ScalarObject-class0.0470.0000.046
addVig2Menu000
anyMissing000
cache0.0010.0020.002
channel0.0890.0170.108
channelNames0.0230.0000.023
class.AnnotatedDataFrame0.0140.0000.014
class.ExpressionSet0.0980.0040.102
class.MIAxE0.0100.0000.011
class.MultiSet0.0140.0000.013
class.NChannelSet0.0730.0000.074
class.Versioned0.0260.0000.027
class.VersionedBiobase0.0130.0000.013
class.Versions0.0050.0000.005
class.VersionsNull000
class.container0.0010.0010.001
class.eSet0.0370.0010.039
classVersion0.0020.0000.002
contents0.0010.0000.001
copyEnv000
copySubstitute0.0050.0020.006
createPackage0.0020.0010.008
data.aaMap0.0000.0010.001
data.geneData0.0110.0020.013
data.reporter0.0010.0000.000
data.sample.ExpressionSet0.0090.0000.008
data.sample.MultiSet0.0020.0010.003
dumpPackTxt0.0000.0000.002
esApply0.5670.0060.573
getPkgVigs0.0040.0020.009
isCurrent0.0150.0000.014
isUnique000
isVersioned0.0050.0000.006
lcSuffix0.0000.0000.001
listLen000
makeDataPackage0.0450.0020.049
matchpt0.0030.0000.003
multiassign000
note0.0010.0000.000
openPDF000
openVignette000
package.version000
read.AnnotatedDataFrame0.0050.0010.007
read.MIAME0.0010.0000.001
readExpressionSet0.0280.0010.033
reverseSplit000
rowMedians0.0200.0010.022
rowQ0.0090.0030.012
selectChannels0.0200.0010.022
selectSome000
strbreak0.0010.0000.000
subListExtract0.4610.0110.473
testBioCConnection0.0290.0070.354
updateOldESet000
validMsg000