Question: error in RNA-Seq workflow at the gene level
0
gravatar for hope-dream
4.2 years ago by
hope-dream0
hope-dream0 wrote:

In the RNA-Seq workflow: gene-level exploratory analysis and differential expression

 

source('http://www.bioconductor.org/help/workflows/rnaseqGene/rnaseqGene.R')

in this step, the error appear,
se <- summarizeOverlaps(features=genes, reads=bamfiles,
                        mode="Union",
                        singleEnd=FALSE,
                        ignore.strand=TRUE,
                        fragments=TRUE )

 

 

Error: 8 errors; first error:
  Error in findOverlaps(query, grglist(unlist(subject, use.names = FALSE)), : error in evaluating the argument 'subject' in selecting a method for function 'findOverlaps': Error in .Call2("cigar_ranges", cigar, flag, space, pos, f, ops, drop.empty.ranges,  : 
  function '_new_RangeAE' not provided by package 'S4Vectors'

For more information, use bplasterror(). To resume calculation, re-call the function and
  set the argument 'BPRESUME' to TRUE or wrap the previous call in bpresume().

First traceback:
  42: source("http://www.bioconductor.org/help/workflows/rnaseqGene/rnaseqGene.R")
  41: withVisible(eval(ei, envir))
  40: eval(ei, envir)
  39: eval(expr, envir, enclos)
  38: summarizeOverlaps(features = genes, reads = bamfiles, mode = "Union", 
          singleEnd = FALSE, ignore.strand = TRUE, fragments = TRUE)
  37: summarizeOverlaps(features = genes, reads = bamfiles, mode = "Union", 
          singleEnd = FALSE, ignore.strand = TRUE, fragments = TR
In addition: Warning messages:
1: 'makeTranscriptDbFromGFF' is deprecated.
Use 'makeTxDbFromGFF' instead.
See help("Deprecated") 
2: In matchCircularity(seqlevels(gr), circ_seqs) :
  None of the strings in your circ_seqs argument match your seqnames.

 

 

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

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] stats4    parallel  graphics  grDevices utils     datasets  stats     methods   base     

other attached packages:
 [1] BiocInstaller_1.18.3    knitr_1.10.5            BiocStyle_1.6.0         GenomicAlignments_1.4.1
 [5] GenomicFeatures_1.20.1  AnnotationDbi_1.30.1    Biobase_2.28.0          Rsamtools_1.20.4       
 [9] Biostrings_2.36.1       XVector_0.8.0           airway_0.102.0          GenomicRanges_1.20.5   
[13] GenomeInfoDb_1.4.0      IRanges_2.2.4           S4Vectors_0.6.0         BiocGenerics_0.14.0    
[17] readr_0.1.1             sqldf_0.4-10            RSQLite_1.0.0           DBI_0.3.1              
[21] gsubfn_0.6-6            proto_0.3-10            dplyr_0.4.1             plyr_1.8.3             

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.6        bitops_1.0-6       base64enc_0.1-2    iterators_1.0.7    BatchJobs_1.6     
 [6] tools_3.2.0        zlibbioc_1.14.0    biomaRt_2.24.0     digest_0.6.8       checkmate_1.5.3   
[11] foreach_1.4.2      rtracklayer_1.28.4 stringr_1.0.0.9000 tcltk_3.2.0        XML_3.98-1.2      
[16] fail_1.2           BiocParallel_1.2.3 sendmailR_1.2-1    magrittr_1.5       BBmisc_1.9        
[21] codetools_0.2-11   assertthat_0.1     brew_1.0-6         stringi_0.4-1      RCurl_1.95-4.6    
[26] chron_2.3-45 

how to solve the proble???

 

 

genomicalignments rnaseqgene • 1.3k views
ADD COMMENTlink modified 4.2 years ago by Dan Tenenbaum8.2k • written 4.2 years ago by hope-dream0
Answer: error in RNA-Seq workflow at the gene level
2
gravatar for Michael Love
4.2 years ago by
Michael Love25k
United States
Michael Love25k wrote:

I'm not sure the cause of this error, because the major package version numbers match the sessionInfo() from the workflow.

Just a guess: can you try adding this line above the summarizeOverlaps() call:

library(BiocParallel)
register(SerialParam())
ADD COMMENTlink written 4.2 years ago by Michael Love25k

thanks for your help, I have solved the problem when restart the r session, but I don't know why.

ADD REPLYlink written 4.2 years ago by hope-dream0
Answer: error in RNA-Seq workflow at the gene level
2
gravatar for Vincent
4.2 years ago by
Vincent20
France
Vincent20 wrote:

Hi,

I've got the same error. This error is due to version of "S4Vectors" package. In my computer i can run this code with the version 0.4.0 (instead of 0.6.0) without error.

This is very embarrassing because I need S4Vectors >= 0.5.0 for another packages ("ShortRead"). It is possible to have 2 versions for one package ?

Hope this help !

ADD COMMENTlink written 4.2 years ago by Vincent20

I'm not sure this alone is the explanation, because it runs on the workflow machine without error and using S4Vectors_0.6.0 (see the bottom of the page here)

http://bioconductor.org/help/workflows/rnaseqGene/

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Michael Love25k
1

I just ran the summarizeOverlaps() call from the workflow on my machine without error. Maybe this will help us identify the issue.

My session info:

R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

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] stats4    parallel  stats     graphics  grDevices datasets  utils     methods  
[9] base     

other attached packages:
 [1] GenomicAlignments_1.4.1 GenomicFeatures_1.20.1  AnnotationDbi_1.30.1   
 [4] Biobase_2.28.0          Rsamtools_1.20.4        Biostrings_2.36.1      
 [7] XVector_0.8.0           airway_0.102.0          GenomicRanges_1.20.5   
[10] GenomeInfoDb_1.4.0      IRanges_2.2.4           S4Vectors_0.6.0        
[13] BiocGenerics_0.14.0     testthat_0.10.0         devtools_1.8.0         
[16] knitr_1.10.5            BiocInstaller_1.18.3   

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.6          xml2_0.1.1           zlibbioc_1.14.0     
 [4] BiocParallel_1.2.3   tools_3.2.0          snow_0.3-13         
 [7] DBI_0.3.1            lambda.r_1.1.7       futile.logger_1.4.1 
[10] git2r_0.10.1         rversions_1.0.1      digest_0.6.8        
[13] crayon_1.3.0         rtracklayer_1.28.4   futile.options_1.0.0
[16] bitops_1.0-6         biomaRt_2.24.0       RCurl_1.95-4.6      
[19] curl_0.8             RSQLite_1.0.0        memoise_0.2.1       
[22] XML_3.98-1.2        
ADD REPLYlink written 4.2 years ago by Michael Love25k

thanks for your help, I have solved the problem when restart the r session, but I don't know why.

ADD REPLYlink written 4.2 years ago by hope-dream0
1

Hi,

There is a serious gotcha with sessionInfo(): if you update a package that is already attached or loaded into your session, and run sessionInfo() right after that, it reports the version of the new installed package but in fact you're still using the old one. This is until you restart the session. This is why it is highly recommended that you update your packages before loading any package (except BiocInstaller of course, which is needed to run biocLite()), or to restart R after updating your packages.

So in your case for example, maybe you updated some of your packages (including an old version of S4Vectors) right before the call to summarizeOverlaps() that gave you the function '_new_RangeAE' not provided by package 'S4Vectors' error? If that's the case, then your were still using the old version of S4Vectors despite sessionInfo() reporting that you were using the latest version.

There is a note in the man page of sessionInfo() about this:

  • The information on ‘loaded’ packages and namespaces is the _current_ version installed at the location the package was loaded from: it can be wrong if another process has been changing packages during the session.

So, following some long tradition in R, that sort of makes it a feature and you're not allowed to complain about it anymore ;-) Even though that note kind of contradicts what the description section says at the top of the man page:

  • Print version information about R, the OS and attached or loaded packages.

and also contradicts the name of the function itself (sessionInfo).

Anyway I wonder if we shouldn't try to make biocLite() a little bit smarter so it prints a message after completing the update process to tell the user to restart the session (but only if one of the packages that was already attached or loaded got updated).

H.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Hervé Pagès ♦♦ 14k

Thanks for your help. My version of R is 3.1.2, i think i need to update to 3.2.0

ADD REPLYlink written 4.2 years ago by Vincent20
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