Build/check report for BioC 3.23 - CHECK results for Biobase on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4774
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*

CHECK results for Biobase on nebbiolo1

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.

raw results

Summary

Package: Biobase

Version: 2.71.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Biobase.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Biobase_2.71.0.tar.gz

StartedAt: 2025-10-31 21:26:45 -0400 (Fri, 31 Oct 2025)

EndedAt: 2025-10-31 21:28:07 -0400 (Fri, 31 Oct 2025)

EllapsedTime: 82.1 seconds

RetCode: 0

Status: OK

CheckDir: Biobase.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Biobase.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Biobase_2.71.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/Biobase.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘2.71.0’
* 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: ‘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 ... 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
  ‘/home/biocbuild/bbs-3.23-bioc/meat/Biobase.Rcheck/00check.log’
for details.

Installation output

Biobase.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Biobase
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘Biobase’ ...
** this is package ‘Biobase’ version ‘2.71.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/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/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o Biobase.so Rinit.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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 -- Fri Oct 31 21:27:31 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 
 10.535   0.130  10.664

Biobase.Rcheck/tests/test-rowMedians.Rout


R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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(): 0.291
Random test #2
rowMedians()/apply(): 0.179
rowMedians()/rowMedians2(): 0.333
Random test #3
rowMedians()/apply(): 0.0588
Random test #4
rowMedians()/apply(): 0.223
rowMedians()/rowMedians2(): 0.333
Random test #5
rowMedians()/apply(): 0.272
rowMedians()/rowMedians2(): 0.346
Random test #6
rowMedians()/apply(): 0.326
rowMedians()/rowMedians2(): 0.375
Random test #7
rowMedians()/apply(): 0.309
Random test #8
rowMedians()/apply(): 0
rowMedians()/rowMedians2(): NaN
Random test #9
rowMedians()/apply(): 0.25
Random test #10
rowMedians()/apply(): 0.0811
Random test #11
rowMedians()/apply(): 0.188
Random test #12
rowMedians()/apply(): 0.154
Random test #13
rowMedians()/apply(): 0.4
rowMedians()/rowMedians2(): 0.857
Random test #14
rowMedians()/apply(): 0.26
Random test #15
rowMedians()/apply(): 0.255
Random test #16
rowMedians()/apply(): 0.198
rowMedians()/rowMedians2(): 0.409
Random test #17
rowMedians()/apply(): 0.2
Random test #18
rowMedians()/apply(): 0.16
rowMedians()/rowMedians2(): 0.75
Random test #19
rowMedians()/apply(): 0.37
rowMedians()/rowMedians2(): 0.694
Random test #20
rowMedians()/apply(): 0.254
rowMedians()/rowMedians2(): 0.385
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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  608522 32.5    1223758 65.4  1111239 59.4
Vcells 2115078 16.2   12255594 93.6 12354150 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  608538 32.5    1223758 65.4  1223758 65.4
Vcells 2116095 16.2   12255594 93.6 12354150 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  608538 32.5    1223758 65.4  1223758 65.4
Vcells 2115220 16.2   12255594 93.6 12354150 94.3
> stopifnot(all.equal(y0,y1))
> cat(sprintf("rowMedians()/apply(): %.3g\n", (t1/t0)[3]))
rowMedians()/apply(): 0.236
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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 
 19.815   0.286  20.091

Example timings

Biobase.Rcheck/Biobase-Ex.timings

name	user	system	elapsed
Aggregate	0.005	0.000	0.006
ScalarObject-class	0.019	0.000	0.019
addVig2Menu	0.001	0.000	0.000
anyMissing	0.000	0.000	0.001
cache	0.003	0.001	0.003
channel	0.192	0.017	0.210
channelNames	0.040	0.002	0.042
class.AnnotatedDataFrame	0.022	0.001	0.023
class.ExpressionSet	0.155	0.006	0.161
class.MIAxE	0.014	0.002	0.016
class.MultiSet	0.022	0.001	0.022
class.NChannelSet	0.129	0.000	0.129
class.Versioned	0.046	0.000	0.046
class.VersionedBiobase	0.02	0.00	0.02
class.Versions	0.010	0.000	0.009
class.VersionsNull	0.000	0.000	0.001
class.container	0.002	0.000	0.002
class.eSet	0.071	0.001	0.072
classVersion	0.003	0.001	0.004
contents	0.001	0.000	0.001
copyEnv	0	0	0
copySubstitute	0.007	0.001	0.008
createPackage	0.002	0.002	0.005
data.aaMap	0.000	0.001	0.002
data.geneData	0.017	0.002	0.019
data.reporter	0.001	0.001	0.001
data.sample.ExpressionSet	0.009	0.002	0.011
data.sample.MultiSet	0.005	0.000	0.004
dumpPackTxt	0.000	0.001	0.001
esApply	0.911	0.008	0.918
getPkgVigs	0.010	0.003	0.012
isCurrent	0.021	0.004	0.025
isUnique	0.001	0.000	0.001
isVersioned	0.009	0.002	0.011
lcSuffix	0.001	0.000	0.001
listLen	0	0	0
makeDataPackage	0.059	0.004	0.063
matchpt	0.005	0.001	0.005
multiassign	0.001	0.000	0.000
note	0	0	0
openPDF	0	0	0
openVignette	0	0	0
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.009	0.001	0.011
read.MIAME	0.002	0.000	0.002
readExpressionSet	0.045	0.000	0.046
reverseSplit	0.001	0.000	0.001
rowMedians	0.024	0.010	0.034
rowQ	0.014	0.007	0.021
selectChannels	0.064	0.001	0.065
selectSome	0.001	0.000	0.000
strbreak	0.000	0.001	0.001
subListExtract	0.638	0.013	0.651
testBioCConnection	0.048	0.004	0.218
updateOldESet	0	0	0
validMsg	0.001	0.000	0.000