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Biobase: Base functions for Bioconductor

Home Page: https://bioconductor.org/packages/Biobase

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biobase's Introduction

Biobase is an R/Bioconductor package that implements base functions for Bioconductor.

See https://bioconductor.org/packages/Biobase for more information including how to install the release version of the package (please refrain from installing directly from GitHub).

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mukhyala henrikbengtsson staticknight37 p-smirnov raoulkam hsadia538 miguelraz mcarlsn villafup kevinushey

biobase's Issues

One occurrence of `F` -> `FALSE`

I spotted:

Biobase/R/methods-container.R

Line 7 in c6470fc

function(x, i, j, ..., drop = F) {

I grep -E "\b(F|T)\b" R/*.R and only found the above.

Biobase failed staged install check on WSL Ubuntu

I am running Ubuntu 18.04 on the Windows Subsystem for Linux. When I tried to install Biobase, it failed the staged install check. A previous StackOverflow post reported the same issue. Note that there is something specific about Biobase. For example, Rsubread, which also has compiled code, passed the staged install check and installs without issue.

> BiocManager::install("Biobase")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'Biobase'
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/Biobase_2.46.0.tar.gz'
Content type 'application/x-gzip' length 1657663 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘Biobase’ ...
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c envir.c -o envir.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib/R/lib -lR
installing to /home/demo/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-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
mv: cannot move '/home/demo/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Biobase/00new/Biobase' to '/home/demo/R/x86_64-pc-linux-gnu-library/3.6/Biobase': Permission denied
ERROR:   moving to final location failed

The downloaded source packages are in
        ‘/tmp/RtmpKotcjP/downloaded_packages’
Installation path not writeable, unable to update packages: curl, farver,
  processx, rprojroot, xfun, class, foreign, nlme
Warning message:
In install.packages(...) :
  installation of package ‘Biobase’ had non-zero exit status
> Sys.setenv(R_INSTALL_STAGED = FALSE)
> BiocManager::install("Biobase")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'Biobase'
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/Biobase_2.46.0.tar.gz'
Content type 'application/x-gzip' length 1657663 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘Biobase’ ...
** using non-staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c envir.c -o envir.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib/R/lib -lR
installing to /home/demo/R/x86_64-pc-linux-gnu-library/3.6/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
* DONE (Biobase)

The downloaded source packages are in
        ‘/tmp/RtmpKotcjP/downloaded_packages’
Installation path not writeable, unable to update packages: curl, farver,
  processx, rprojroot, xfun, class, foreign, nlme
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.6.3      tools_3.6.3

New ExpressionSet does not support sparse matrix?

Hi,
I noticed there has been an update on the biobase. It appears now when I try to create an expressionSet with sparse matrix I get following error:

obj <- new("ExpressionSet", exprs = exprs(eset)) # exprs(eset) was a sparse matrix from an old eset object
Error: unable to find an inherited method for function ‘annotatedDataFrameFrom’ for signature ‘object = "dgCMatrix"’

So what is the recommended approach now for dealing with large sparse data matrix with ExpressionSet class?

MEMORY: rep(NA, ...) -> rep(NA_character_, ...)

In master branch (commit 073511c) there are a few rep(NA, ...) that looks like they could (=should) be rep(NA_character_, ...) in order to avoid unecessary coercion from logical to character;

$ grep -F "rep(NA" R/*.R
R/methods-AnnotatedDataFrame.R:            varMetadata <- data.frame(labelDescription = rep(NA, ncol(data)))
R/methods-AnnotatedDataFrame.R:                    rep(NA, nrow(varMetadata))
R/methods-AnnotatedDataFrame.R:    varMetadata[["labelDescription"]] <- as.character(rep(NA, nrow(varLabels)))
R/methods-AnnotatedDataFrame.R:    varMetadata <- data.frame(labelDescription = rep(NA, ncol(data)))
R/methods-AnnotatedDataFrame.R:        varMetadata[["labelDescription"]] <- rep(NA, nrow(varMetadata))

Selecting the same column twice in an ExpressionSet leads to inconsistencies in column names among slots.

I've ran into an issue where: if class(exprs(eset)) is matrix, and in the case that I select, by name, the same column from an ExpressionSet twice, the column names of the ESet and the column names of the exprs(eset) are then out of sync. This occurs because the column names of the ExpressionSet are made unique, while the exprs column names are left duplicated.

Reproducible example here:

> library(Biobase)
> 
> test.mat <- matrix(seq(1,4), nrow=2)
> 
> colnames(test.mat) <- c("A", "B")
> 
> testESet <- ExpressionSet(test.mat)
> 
> DuplicatedColumnESet <- testESet[,c("A", "A")]
> 
> colnames(DuplicatedColumnESet)
[1] "A"   "A.1"
> colnames(exprs(DuplicatedColumnESet))
[1] "A" "A"
> 
> DuplicatedColumnESet[,colnames(DuplicatedColumnESet)]
Error in orig[[nm]][, j, ..., drop = drop] : subscript out of bounds

This feels like a bug/something the subsetting method of ExpressionSet should avoid, as I think DuplicatedColumnESet[,colnames(DuplicatedColumnESet)] should be valid in all cases.

superclass "characterORconnection" not defined in the environment of the object's class

I hope this is the right place to post this issue (please let me know if I should direct it somewhere else):

SInce ~July 22nd, R CMD check fails for my Bioconductor package QuasR (see e.g. https://github.com/fmicompbio/QuasR/actions/runs/232719578), but only on macOS and not on Linux.
On the Bioconductor builders, QuasR checks fine on all platforms.

The error is reproducible also on my personal macOS laptop, and the traceback shows a call from QuasR::preprocessReads to Biobase::mkScalar. Using the Biobase::mkScalar with a character argument, the error can be triggered in a fresh R session:

library(Biobase)
mkScalar("test")

which results in the same kind of error that I see on my laptop and on github for the QuasR package:

Error in validObject(.Object) : 
  invalid class “ScalarCharacter” object: superclass "characterORconnection" not defined in the environment of the object's class

The error persists if I start with a clean R/Bioconductor installation.
Is it possible that there were recent changes to these classes that may have triggered it?
It's unclear to me why the error only presents it self on some systems, but not on others.

Here is my session info:

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Biobase_2.49.0      BiocGenerics_0.35.4

loaded via a namespace (and not attached):
[1] compiler_4.0.2

Footer error on Windows

Error: processing vignette 'BiobaseDevelopment.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'BiobaseDevelopment.tex' failed.
LaTeX errors:
! Undefined control sequence.
\mref #1#2->\htmladdnormallinkfoot 
                                   {#2}{#1}
l.43 
     
--- failed re-building ‘BiobaseDevelopment.Rnw’

Update: Should be resolved in 6dfec83

Receiving a Warning saying Biobase is not available for R version 4.3.1

this is a screenshot of the line of code I'm running and the error message im getting. Is there anything I can do to resolve this? I've installed the latest version of Biocmanager already.

Problems installing Biobase in R 4.0.5

Hi, I'm having problems installing Biobase. I keep getting this error after trying to install this package -

Error in library(Biobase) : there is no package called ‘Biobase’

Before that I get this message -

Bioconductor version 3.12 (BiocManager 1.30.13), R 4.0.5 (2021-03-31)
Installing package(s) 'BiocVersion', 'Biobase'
also installing the dependency ‘BiocGenerics’

And then nothing happens. Any help would be appreciated.

Thanks

Partial argument name: def -> definition

I get:

** inst
** byte-compile and prepare package for lazy loading
Warning in setMethod("[", "container", def = function(x, i, j, ..., drop = F) { :
  partial argument match of 'def' to 'definition'
Calls: <Anonymous> ... tryCatchOne -> doTryCatch -> sys.source -> eval -> eval
** help

when installing Biobase. This stems from:

Biobase/R/methods-container.R

Lines 6 to 10 in 4dd4294

 setMethod("[", "container", 

 def = function(x, i, j, ..., drop = F) { 

 .container(content = content(x), x = x@x[i], locked = locked(x)) 

 } 

 )

where argument definition is addressed using def.

Biobase bugs since new R version (4.0)

Good morning,

I have a issue with Biobase inside clValid function (clValid package) since I updated R (new version= 4.0).
Below is the error that I obtain :

Error in switch(class(obj), matrix = mat <- obj, ExpressionSet = mat <- Biobase::exprs(obj), :
EXPR doit être un vecteur de longueur 1

The data that I use is a numeric dataframe. Even when I transformed it in a matrix, I obtained the same error.

I try this step that I saw in of the other issues :
exp <- Biobase::exprs(score.SPA.PROGvsPRE)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘exprs’ for signature ‘"matrix"

I check if my object for clValid was valid with validObject(score.SPA.PROGvsPRE), and it's valid.

I try to update Biobase but nothing changes, I have the same problem.

Thank you for your help

Emmanuelle

exprs<- not working anymore

Hi, I am having some issue with version Biobase 2.38.0
while doing :

exp <- exprs(gse)
exprs(gse)<- exp

I am now getting the following error:
Error in (function (od, vd) :
object and replacement value dimnames differ

	setMethod("[", "container",
	def = function(x, i, j, ..., drop = F) {
	.container(content = content(x), x = x@x[i], locked = locked(x))
	}
	)