benilton / oligoclasses Goto Github PK

Hi,
I have been using the oligo package for many years but today, with the release of R 4.0.0, I encountered the following problem when trying to reinstall it:

Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, :
no definition was found for superclass “RangedData” in the specification of class “RangedDataCopyNumber”

I would really apreciate any feedbak because I cannot find a way through it.

Thanks.

I enclose the code for the whole installation process:

Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'oligo'
also installing the dependency ‘oligoClasses’
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘oligo’

installing the source packages ‘oligoClasses’, ‘oligo’

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/oligoClasses_1.51.0.tar.gz'
Content type 'application/x-gzip' length 373251 bytes (364 KB)

downloaded 364 KB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/oligo_1.53.0.tar.gz'
Content type 'application/x-gzip' length 28421038 bytes (27.1 MB)

downloaded 27.1 MB

• installing source package ‘oligoClasses’ ...
  ** using staged installation
  ** R
  ** data
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, :
  no definition was found for superclass “RangedData” in the specification of class “RangedDataCopyNumber”
  Error: unable to load R code in package ‘oligoClasses’
  Execution halted
  ERROR: lazy loading failed for package ‘oligoClasses’
• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/oligoClasses’
  ERROR: dependency ‘oligoClasses’ is not available for package ‘oligo’
• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/oligo’

The downloaded source packages are in
‘/private/var/folders/tt/f8_2bryn5vbfknlppg9xzsc40000gn/T/Rtmptk1LE5/downloaded_packages’
Warning messages:
1: In install.packages(...) :
installation of package ‘oligoClasses’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘oligo’ had non-zero exit status

Dear developers,
I'm having problems to install oligoClasses, that depends on ff.
Same problem when trying on Mac OS X 10.14.6 and Linux Debian 10

I tried the standard procedure:
BiocManager::install("oligoClasses")

But when trying to load the library, I get the following error:
Error: package or namespace load failed for ‘oligoClasses’: objects ‘open.ff’, ‘close.ff’ are not exported by 'namespace:ff'

It seems that the problem originates in ff.
I'm running R version 4.0.2 (2020-06-22)
In fact, open.ff or close.ff functions are not visible in ff package, despite they appear in the ff package manual. I'm not sure if they should be explicitly visible for oligoClasses to run, or just open and close functions from base are enough.

I'm writing the same question here and in the ff repository issues tab.
My apologies if the question should not be directed here.

Best regards,
Sergio