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This page was generated on 2025-10-07 10:06 -0400 (Tue, 07 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 917
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Package 26/229HostnameOS / ArchINSTALLBUILDCHECK
Biobase 2.69.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2025-10-07 06:00 -0400 (Tue, 07 Oct 2025)
git_url: https://git.bioconductor.org/packages/Biobase
git_branch: devel
git_last_commit: 6711552
git_last_commit_date: 2025-09-12 21:18:58 -0400 (Fri, 12 Sep 2025)
teran2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  

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: 2.69.1
Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:Biobase.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings Biobase_2.69.1.tar.gz
StartedAt: 2025-10-07 07:50:17 -0400 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 07:51:13 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 56.0 seconds
RetCode: 0
Status:   OK  
CheckDir: Biobase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:Biobase.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings Biobase_2.69.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/Biobase.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.69.1’
* 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) 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 ... NOTE
Note: information on .o files is not available
* 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: 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/Biobase.Rcheck/00check.log’
for details.

Installation output

Biobase.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL Biobase
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’
* installing *source* package ‘Biobase’ ...
** this is package ‘Biobase’ version ‘2.69.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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 -- Tue Oct  7 07:50:47 2025 
*********************************************** 
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   0.155   6.307

Biobase.Rcheck/tests/test-rowMedians.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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(): 0.351
Random test #2
rowMedians()/apply(): 0.19
rowMedians()/rowMedians2(): 0.4
Random test #3
rowMedians()/apply(): 0.111
Random test #4
rowMedians()/apply(): 0.267
rowMedians()/rowMedians2(): 0.356
Random test #5
rowMedians()/apply(): 0.373
rowMedians()/rowMedians2(): 0.453
Random test #6
rowMedians()/apply(): 0.414
rowMedians()/rowMedians2(): 0.444
Random test #7
rowMedians()/apply(): 0.401
Random test #8
rowMedians()/apply(): 0
rowMedians()/rowMedians2(): 0
Random test #9
rowMedians()/apply(): 0.4
Random test #10
rowMedians()/apply(): 0.0625
Random test #11
rowMedians()/apply(): 0.214
Random test #12
rowMedians()/apply(): 0.187
Random test #13
rowMedians()/apply(): 0.417
rowMedians()/rowMedians2(): 0.833
Random test #14
rowMedians()/apply(): 0.309
Random test #15
rowMedians()/apply(): 0.319
Random test #16
rowMedians()/apply(): 0.153
rowMedians()/rowMedians2(): 0.355
Random test #17
rowMedians()/apply(): 0.268
Random test #18
rowMedians()/apply(): 0.208
rowMedians()/rowMedians2(): 0.846
Random test #19
rowMedians()/apply(): 0.485
rowMedians()/rowMedians2(): 0.865
Random test #20
rowMedians()/apply(): 0.384
rowMedians()/rowMedians2(): 0.52
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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  607917 32.5    1224567 65.4  1109717 59.3
Vcells 2114011 16.2   12255594 93.6 12350560 94.3
> 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  607933 32.5    1224567 65.4  1224567 65.4
Vcells 2115028 16.2   12255594 93.6 12350560 94.3
> t1 <- system.time({
+   for (rr in 1:20)
+     y1 <- rowMedians(x, na.rm=FALSE)
+ })
> gc()
          used (Mb) gc trigger (Mb) max used (Mb)
Ncells  607933 32.5    1224567 65.4  1224567 65.4
Vcells 2114153 16.2   12255594 93.6 12350560 94.3
> stopifnot(all.equal(y0,y1))
> cat(sprintf("rowMedians()/apply(): %.3g\n", (t1/t0)[3]))
rowMedians()/apply(): 0.268
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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 
 12.786   0.267  13.041

Example timings

Biobase.Rcheck/Biobase-Ex.timings

nameusersystemelapsed
Aggregate0.0030.0000.003
ScalarObject-class0.0070.0000.008
addVig2Menu000
anyMissing000
cache0.0010.0010.002
channel0.1180.0230.140
channelNames0.0260.0020.028
class.AnnotatedDataFrame0.0140.0000.013
class.ExpressionSet0.0940.0060.100
class.MIAxE0.0070.0020.010
class.MultiSet0.0130.0000.013
class.NChannelSet0.0720.0000.072
class.Versioned0.0260.0010.027
class.VersionedBiobase0.0110.0010.012
class.Versions0.0040.0010.005
class.VersionsNull0.0000.0000.001
class.container0.0010.0000.001
class.eSet0.0400.0000.041
classVersion0.0020.0000.002
contents000
copyEnv000
copySubstitute0.0030.0030.006
createPackage0.0020.0010.007
data.aaMap0.0000.0010.001
data.geneData0.0120.0010.013
data.reporter0.0000.0010.001
data.sample.ExpressionSet0.0090.0000.009
data.sample.MultiSet0.0020.0010.003
dumpPackTxt0.0010.0000.003
esApply0.5660.0040.570
getPkgVigs0.0040.0020.008
isCurrent0.0160.0000.016
isUnique000
isVersioned0.0060.0010.006
lcSuffix0.0010.0000.000
listLen0.0000.0000.001
makeDataPackage0.0420.0040.047
matchpt0.0020.0000.002
multiassign0.0010.0000.001
note000
openPDF000
openVignette000
package.version0.0000.0000.001
read.AnnotatedDataFrame0.0050.0000.006
read.MIAME0.0010.0000.001
readExpressionSet0.0230.0010.026
reverseSplit0.0010.0000.000
rowMedians0.0170.0060.023
rowQ0.0080.0040.013
selectChannels0.0340.0000.034
selectSome000
strbreak0.0000.0000.001
subListExtract0.4350.0190.454
testBioCConnection0.0350.0030.573
updateOldESet000
validMsg000