Package ‘GenomicRanges’ version 1.20.8 cannot be unloaded
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@pau-marc-munoz-torres-6731
Last seen 4.9 years ago
Barcelona

library("RAPIDR")

makeBinnedCountsFile(c("nfamele1_sorted.bam","nfamele2_sorted.bam","nMALE1_sorted.bam","nMALE2_sorted.bam","T-SRR611848_1_sorted.bam"),c("nfamele1","nfamele2","nMALE1","nMALE2","T-SRR611848"),"binnedcounts.r",mask=NULL,k=20000)

 

 

I am getting the following error in a script that was working a month before

 

Error in unloadNamespace(package) : 

  namespace ‘GenomicRanges’ is imported by ‘RAPIDR’, ‘GenomicAlignments’, ‘Rsamtools’ so cannot be unloaded

Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,  : 

  Package ‘GenomicRanges’ version 1.20.8 cannot be unloaded

 

rapidr genomicranges • 3.5k views
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This seems like a weird one, in addition to what Herve asks for, you can try to start R in "vanilla" mode, ie. from the terminal launch R via a call like so:

$ R --vanilla

Perhaps there's some issue with R starting up and loading a previously saved workspace (is there an .RData file in the working directory you launch R from (or your home directory(?)). Launching with --vanilla will run R without loading some of these things.

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Ok, I'm sorry. I will write to RAPIDR authors, anyway i do not understand why GenomicRanges changes so much, when i write a program i expect some estability with libraries. This kind of bug is not reported for the first time in Rapidr. My last update of the genomic ranges library was las 19/10, so a week ago

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=hr_HR.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=hr_HR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=hr_HR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=hr_HR.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] RAPIDR_0.1.1

loaded via a namespace (and not attached):
 [1] IRanges_2.2.9           Rsamtools_1.20.4        Biostrings_2.36.4      
 [4] bitops_1.0-6            GenomicAlignments_1.4.1 chron_2.3-47           
 [7] GenomeInfoDb_1.4.3      futile.options_1.0.0    stats4_3.2.2           
[10] zlibbioc_1.14.0         XVector_0.8.0           data.table_1.9.6       
[13] S4Vectors_0.6.6         futile.logger_1.4.1     BiocParallel_1.2.21    
[16] lambda.r_1.1.7          PropCIs_0.2-5           parallel_3.2.2         
[19] BiocGenerics_0.14.0     GenomicRanges_1.20.8   
 

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Are you sure this happens only with the latest GenomicRanges? Btw, the RAPIDR package has some serious issues. From just a short glance at the code, makeBinnedCountsFile() is obviously broken (the line to write out the masked counts is commented out for some reason). Deeper in the code, it calls library() to load a BSgenome package, when it should really be using requireNamespace() (probably related to this bug). It then reads a BED file using read.table and forgets to add 1 to the start positions. And the list goes on.

A likely cause of this error is that R is attempting to attach a package namespace that has already been loaded from a different version of the package. In such cases, it will attempt to unload the old namespace.

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You're using BioC 3.1 which is not supported anymore: the latest release is BioC 3.2 which was released 2 weeks ago. Please update at your earliest convenience. Because BioC 3.2 uses the same version of R as BioC 3.1, updating is as easy as running:

source("http://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")

Note that CRAN packages that depend on BioC packages are at the risk to break when we release a new version of BioC. We have no control on these packages (in particular we didn't have an opportunity to build/check them against the new release) so there is nothing we can do about it. This is why having CRAN packages that depend on BioC packages is fundamentally a broken model but that's another story.

H.

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Thanks you Herve, I will proceed as you suggest

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@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States

Hi,

This support site is for Bioconductor packages. Note that even though RAPIDR depends on several Bioconductor packages (Biostrings, Rsamtools, GenomicRanges, GenomicAlignments), it is itself a CRAN package, not a Bioconductor package. So a better option for you would be to contact its author/maintainer directly.

That being said, you don't give us enough information to help you. We need at least a reproducible example and your sessionInfo(). See our posting guide.

Thanks,

H.

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