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Question: Had to remove duplicated() in order to install GenomicRanges 1.22 on top of 1.20 on linux
0
gravatar for knb
2.1 years ago by
knb0
Germany
knb0 wrote:

I have had the same poblem (now twice) as mentioned in this post (from 2013, by someone else)

http://bioc-devel.r-project.narkive.com/9nMVTTgy/error-installing-genomicranges

** preparing package for lazy loading
Error in fmls[[***@signature]] <- quote(rowData(x)) :
object of type 'symbol' is not subsettable
Error : unable to load R code in package 'GenomicRanges'

Seems that there was a new release GenomicRanges, 1.22.0. of GenomicRanges, and I was not able to install it on top of 1.20. Same error as above.

I was able to "resolve" this by removing the call for generic function "duplicated". Actually I removed a string "duplicated" from a loop in... :

GenomicRanges/R/SummarizedExperiment-rowData-methods.R
SummarizedExperiment/R/RangedSummarizedExperiment-class.R

Specifically, I removed it from  here [in c(...)] in RangedSummarizedExperiment-class.R:

## Single dispatch, generic signature fun(x, ...)                               
local({                                                                         
    .funs <-                                                                    
        c("duplicated",  "end", "end<-", "ranges", "seqinfo", "seqnames",                     
          "start", "start<-", "strand", "width", "width<-")                     
                                                                                                            

GenomicRanges/R/SummarizedExperiment-rowData-methods.R contains a similar block of code, and I removed duplicated from the c() Vector as well.

For no apparent reason, R interprets a call to "duplicated()" as a symbol and not as a function. No Idea why this is so; and don't know which "duplicated" causes the bug at installation time.

showMethods("duplicated") now gives this result on my problematic computer:

x="ANY"
x="CompressedIntegerList"
x="CompressedList"
x="DataTable"
x="Dups"
x="GenomicRanges"
x="List"
x="Rle"
x="Vector"
x="XRawList"

and on a computer where SummarizedExperiment 1.0.0 and is depedecy GenomicRanges 1.22 can be properly installed,

showMethods("duplicated") now gives this result:

x="ANY"
x="CompressedIntegerList"
x="CompressedList"
x="DataTable"
x="Dups"
x="GenomicRanges"
x="List"
x="RangedSummarizedExperiment"
x="Rle"
x="SummarizedExperiment"
x="Vector"
x="XRawList"

How can I really resolve the issue? What might be wrong with duplicated()?. My R was installed from source

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.04

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

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] airway_0.104.0             SummarizedExperiment_1.0.0 Biobase_2.30.0             GenomicRanges_1.22.0      
 [5] GenomeInfoDb_1.6.0         IRanges_2.4.0              S4Vectors_0.8.0            BiocGenerics_0.16.0       
 [9] BiocInstaller_1.20.0       colorout_1.1-1            

loaded via a namespace (and not attached):
 [1] coin_1.1-0        lattice_0.20-33   codetools_0.2-14  mvtnorm_1.0-3     zoo_1.7-12        grid_3.2.2       
 [7] zlibbioc_1.16.0   XVector_0.10.0    multcomp_1.4-1    party_1.0-23      strucchange_1.5-1 sandwich_2.3-4   
[13] splines_3.2.2     TH.data_1.0-6     survival_2.38-3   modeltools_0.2-21

Built the tar,gz file and installed with R CMD INSTALL

source("http://www.bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help
> biocValid()
[1] TRUE
ADD COMMENTlink modified 24 months ago • written 2.1 years ago by knb0

While your changes to the package code might have allowed it to be installed, it is not the source of the problem. I'd suggest that you remove your patched version remove.packages("GenomicRanges") then start a new R session from the command line and using the --vanilla option, so that no additional packages are loaded and no other software is getting in the way. It would then be helpful to report exactly what happens, so for me

$ R --vanilla
> biocLite("GenomicRanges")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.0), R 3.2.2 Patched (2015-10-11
  r69513).
Installing package(s) ‘GenomicRanges’
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/GenomicRanges_1.22.0.tar.gz'
Content type 'application/x-gzip' length 926760 bytes (905 KB)
==================================================
downloaded 905 KB

* installing *source* package ‘GenomicRanges’ ...
** libs
clang-3.5 -std=gnu99 -D_FORTIFY_SOURCE=2 -I/home/mtmorgan/bin/R-3-2-branch/include -DNDEBUG  -I/usr/local/include -I"/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/S4Vectors/include" -I"/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/IRanges/include"   -fpic  -ggdb -O0 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
clang-3.5 -std=gnu99 -D_FORTIFY_SOURCE=2 -I/home/mtmorgan/bin/R-3-2-branch/include -DNDEBUG  -I/usr/local/include -I"/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/S4Vectors/include" -I"/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/IRanges/include"   -fpic  -ggdb -O0 -Wall -pedantic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
clang-3.5 -std=gnu99 -D_FORTIFY_SOURCE=2 -I/home/mtmorgan/bin/R-3-2-branch/include -DNDEBUG  -I/usr/local/include -I"/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/S4Vectors/include" -I"/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/IRanges/include"   -fpic  -ggdb -O0 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang-3.5 -std=gnu99 -D_FORTIFY_SOURCE=2 -I/home/mtmorgan/bin/R-3-2-branch/include -DNDEBUG  -I/usr/local/include -I"/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/S4Vectors/include" -I"/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/IRanges/include"   -fpic  -ggdb -O0 -Wall -pedantic -c transcript_utils.c -o transcript_utils.o
clang-3.5 -std=gnu99 -D_FORTIFY_SOURCE=2 -shared -L/home/mtmorgan/bin/R-3-2-branch/lib -L/usr/local/lib64 -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/home/mtmorgan/bin/R-3-2-branch/lib -lR
installing to /home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/GenomicRanges/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicRanges)

The downloaded source packages are in
    ‘/tmp/RtmpYbgRSj/downloaded_packages’
> 

 

ADD REPLYlink written 2.1 years ago by Martin Morgan ♦♦ 20k

I tried R --vanilla as local user, I tried it as root, I removed GenomicRanges subdirectory, tried both again. I experimented with setting .libPaths(). I removed all R installations in /usr/{lib,bin...} and now use /usr/local and a personal library in my /home directory.

The error  did never go away, whatever I did.

ADD REPLYlink written 2.1 years ago by knb0

But can you please do as I asked and demonstrated, and report the transcript of the session? And please use remove.packages("GenomicRanges"), repeating as necessary until told that there is no package to remove. And for good measure report the output of traceback() and sessionInfo() after the error.

ADD REPLYlink written 2.1 years ago by Martin Morgan ♦♦ 20k

added below

ADD REPLYlink written 2.1 years ago by knb0
0
gravatar for knb
2.1 years ago by
knb0
Germany
knb0 wrote:
 R --vanilla
> remove.packages("GenomicRanges")  # actually removed the directory
Removing package from ‘/home/knut/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
> source("http://www.bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help
> biocLite("GenomicRanges")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.0), R 3.2.2 (2015-08-14).
Installing package(s) ‘GenomicRanges’
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/GenomicRanges_1.22.0.tar.gz'
Content type 'application/x-gzip' length 926760 bytes (905 KB)
==================================================
downloaded 905 KB

* installing *source* package ‘GenomicRanges’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/home/knut/R/x86_64-pc-linux-gnu-library/3.2/S4Vectors/include" -I"/home/knut/R/x86_64-pc-linux-gnu-library/3.2/IRanges/include"   -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/home/knut/R/x86_64-pc-linux-gnu-library/3.2/S4Vectors/include" -I"/home/knut/R/x86_64-pc-linux-gnu-library/3.2/IRanges/include"   -fpic  -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/home/knut/R/x86_64-pc-linux-gnu-library/3.2/S4Vectors/include" -I"/home/knut/R/x86_64-pc-linux-gnu-library/3.2/IRanges/include"   -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/home/knut/R/x86_64-pc-linux-gnu-library/3.2/S4Vectors/include" -I"/home/knut/R/x86_64-pc-linux-gnu-library/3.2/IRanges/include"   -fpic  -g -O2  -c transcript_utils.c -o transcript_utils.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/usr/local/lib/R/lib -lR
installing to /home/knut/R/x86_64-pc-linux-gnu-library/3.2/GenomicRanges/libs
** R
** inst
** preparing package for lazy loading
Error in fmls[[generic@signature]] <- quote(rowRanges(x)) :
  object of type 'symbol' is not subsettable
Error : unable to load R code in package ‘GenomicRanges’
ERROR: lazy loading failed for package ‘GenomicRanges’
* removing ‘/home/knut/R/x86_64-pc-linux-gnu-library/3.2/GenomicRanges’

The downloaded source packages are in
    ‘/tmp/Rtmp3mXH1k/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
> traceback()
No traceback available
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.04

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

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

other attached packages:
[1] BiocInstaller_1.20.0

loaded via a namespace (and not attached):
[1] tools_3.2.2
ADD COMMENTlink modified 2.1 years ago by Martin Morgan ♦♦ 20k • written 2.1 years ago by knb0

It's a mystery to me. Is R at the command line an alias? accessing the location you think it should? So the output of

$ alias R
$ which R

and perhaps also, within a new R session,

> search()
[1] ".GlobalEnv"        "package:stats"     "package:graphics" 
[4] "package:grDevices" "package:utils"     "package:datasets" 
[7] "package:methods"   "Autoloads"         "package:base"     

In a new R session, no --vanilla, I think the code should be doing something like the following

library(BiocGenerics)
tmpl <- function() {}
generic <- getGeneric("duplicated")
formals(tmpl) <- formals(generic)
fmls <- as.list(formals(tmpl))
fmls[] <- sapply(names(fmls), as.symbol)
fmls[[generic@signature]]

Does the above reproduce the error? If so, can you step through each line and report the value created? If not, can you try adding, one at a time and trying again

library(S4Vectors)
library(IRanges)
library(GenomeInfoDb)
library(XVector)

after library(BiocGenerics) ?

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Martin Morgan ♦♦ 20k
0
gravatar for knb
2.1 years ago by
knb0
Germany
knb0 wrote:

Part 1 of 2:

R> .libPaths()
[1] "/home/knb/R/x86_64-pc-linux-gnu-library/3.2" "/usr/local/lib64/R/library"                 
R> q()

 wb3 in ~
○ → which R
/usr/local/bin/R

my R command was indeed aliased to something. However, unaliasing does not solve the problem.

while in ~

○ → which R
/usr/local/bin/R

while in ~

○ → alias R
alias R='R --no-save --silent'

while in ~

○ → unalias R

while in ~

○ → alias R
bash: alias: R: not found

while in ~

○ → R --vanilla

(attempt to install GenomicRanges results in same output as above)

ADD COMMENTlink modified 2.1 years ago by Martin Morgan ♦♦ 20k • written 2.1 years ago by knb0
0
gravatar for knb
2.1 years ago by
knb0
Germany
knb0 wrote:

Part 2 of 2:

In a new R session

Problematic computer:

R> library(BiocGenerics)
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unlist, unsplit

R> tmpl <- function() {}
R> generic <- getGeneric("duplicated")
R> formals(tmpl) <- formals(generic)
R> fmls <- as.list(formals(tmpl))
R> fmls[] <- sapply(names(fmls), as.symbol)
R> fmls[[generic@signature]]
x

 

Computer with GenomicRanges properly installed:

 search()
 [1] ".GlobalEnv"        "package:stats"     "package:graphics"  "package:grDevices" "package:utils"    
 [6] "package:datasets"  "package:colorout"  ".startup"          "package:methods"   "Autoloads"        
[11] "package:base"       
R> search()
 [1] ".GlobalEnv"        "package:stats"     "package:graphics"  "package:grDevices" "package:utils"    
 [6] "package:datasets"  "package:colorout"  ".startup"          "package:methods"   "Autoloads"        
[11] "package:base"     
R> library(BiocGenerics)
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
    parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff,
    sort, table, tapply, union, unique, unlist, unsplit

R> tmpl <- function() {}
R> generic <- getGeneric("duplicated")
R> formals(tmpl) <- formals(generic)
R> fmls <- as.list(formals(tmpl))
R> fmls[] <- sapply(names(fmls), as.symbol)
R> fmls[[generic@signature]]
x

On problematic computer, In another new R session, replacing "duplicated" with "start":

R> tmpl <- function() {}
R> generic <- getGeneric("start")
R> formals(tmpl) <- formals(generic)
R> fmls <- as.list(formals(tmpl))
R> fmls[] <- sapply(names(fmls), as.symbol)
R> fmls[[generic@signature]]
x

 

 

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by knb0
1

I can't figure this out from here. My best guess is that a package is out of date, or that a .RData or .Rprofile or other file is being referenced that is interfering with installation. The original report solved this by re-installing all packages, which is a bit extreme and doesn't help to identify what the problem is so that a more precise solution can be found.

You could try to edit GenomicRanges/R/SummarizedExperiment-rowData-methods.R so that it prints out the value of what is supposed to be the 'duplicated' generic, and the formals that the code is trying to manipulate. I have changed SummarizedExperiment-rowData-methods.R so that it looks like

    for (.fun in .funs) {
        generic <- getGeneric(.fun)
        if (.fun == "duplicated") print(generic)
        formals(tmpl) <- formals(generic)
        fmls <- as.list(formals(tmpl))
        if (.fun == "duplicated") { print("before"); str(fmls) }
        fmls[] <- sapply(names(fmls), as.symbol)
        if (.fun == "duplicated") { print("after"); str(fmls) }
        fmls[[generic@signature]] <- quote(rowRanges(x))

and then when I install it with install.packages("GenomicRanges", repos=NULL) I see

> install.packages("GenomicRanges", repos=NULL)
Installing package into '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/devel'
(as 'lib' is unspecified)
Bioconductor version 3.3 (BiocInstaller 1.21.1), ?biocLite for help
* installing *source* package 'GenomicRanges' ...
** libs
make: Nothing to be done for `all'.
installing to /home/mtmorgan/R/x86_64-unknown-linux-gnu-library/devel/GenomicRanges/libs
** R
** inst
** preparing package for lazy loading
function (x, incomparables = FALSE, ...) 
standardGeneric("duplicated")
<environment: 0x2be4768>
attr(,"generic")
[1] "duplicated"
attr(,"generic")attr(,"package")
[1] "BiocGenerics"
attr(,"package")
[1] "BiocGenerics"
attr(,"group")
list()
attr(,"valueClass")
character(0)
attr(,"signature")
[1] "x"
attr(,"default")
Method Definition (Class "derivedDefaultMethod"):

function (x, incomparables = FALSE, ...) 
UseMethod("duplicated")
<bytecode: 0x2be3bd8>
<environment: namespace:base>

Signatures:
        x    
target  "ANY"
defined "ANY"
attr(,"skeleton")
(function (x, incomparables = FALSE, ...) 
UseMethod("duplicated"))(x, incomparables, ...)
attr(,"class")
[1] "standardGeneric"
attr(,"class")attr(,"package")
[1] "methods"
[1] "before"
List of 3
 $ x            : symbol 
 $ incomparables: logi FALSE
 $ ...          : symbol 
[1] "after"
List of 3
 $ x            : symbol x
 $ incomparables: symbol incomparables
 $ ...          : symbol ...
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.3 (BiocInstaller 1.21.1), ?biocLite for help
* DONE (GenomicRanges)

 

ADD REPLYlink written 2.1 years ago by Martin Morgan ♦♦ 20k
0
gravatar for knb
24 months ago by
knb0
Germany
knb0 wrote:

Meanwhile, I have installed RUnit, and the many dependencies required to run the testsuite on GenomicRanges 1.22.1 and then I've run this command: duplicated() was NOT commented out in

 ./R/SummarizedExperiment-rowData-methods.R

 

Rscript tests/GenomicRanges_unit_tests.R

Result:

 #  Useful aliases are in env '.startup', Functions in env 'util'.

Loading required package: GenomicRanges
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
    parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff,
    sort, table, tapply, union, unique, unlist, unsplit

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] TRUE
Warning messages:
1: In end(x) > x_seqlengths[x_seqnames_id] :
  longer object length is not a multiple of shorter object length
2: In start(x) < 1L | end(x) > x_seqlengths[x_seqnames_id] :
  longer object length is not a multiple of shorter object length
Timing stopped at: 0 0 0
Error in getMethod(.fun, "SummarizedExperiment") :
  no method found for function 'duplicated' and signature SummarizedExperiment
Timing stopped at: 0.028 0 0.028
Error in substr(digest(getGeneric(.fun)(x)), 1, 5) :
  error in evaluating the argument 'x' in selecting a method for function 'substr': Error in base::match(x, table, nomatch = nomatch, incomparables = incomparables,  :
  'match' requires vector arguments
Calls: digest ... <Anonymous> -> <Anonymous> -> match -> match -> <Anonymous>

Note: method with signature ‘Vector#Vector’ chosen for function ‘split’,
 target signature ‘RangedSummarizedExperiment#Rle’.
 "RangedSummarizedExperiment#ANY" would also be valid

RUNIT TEST PROTOCOL -- Thu Nov 26 00:27:48 2015
***********************************************
Number of test functions: 63
Number of errors: 2
Number of failures: 0

 
1 Test Suite :
GenomicRanges RUnit Tests - 63 test functions, 2 errors, 0 failures
ERROR in test_SummarizedExperiment_GRanges_API: Error in getMethod(.fun, "SummarizedExperiment") :
  no method found for function 'duplicated' and signature SummarizedExperiment
ERROR in test_SummarizedExperiment_GRanges_values: Error in substr(digest(getGeneric(.fun)(x)), 1, 5) :
  error in evaluating the argument 'x' in selecting a method for function 'substr': Error in base::match(x, table, nomatch = nomatch, incomparables = incomparables,  :
  'match' requires vector arguments
Calls: digest ... <Anonymous> -> <Anonymous> -> match -> match -> <Anonymous>

Test files with failing tests

   test_SummarizedExperiment-rowData-methods.R
     test_SummarizedExperiment_GRanges_API
     test_SummarizedExperiment_GRanges_values

Error in BiocGenerics:::testPackage("GenomicRanges") :
  unit tests failed for package GenomicRanges
Calls: <Anonymous> -> <Anonymous>
Execution halted

 

---------------------------------------------------------------------------------------------------------------------------------

biocValid()

* sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.10

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

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

other attached packages:
[1] BiocInstaller_1.20.1

loaded via a namespace (and not attached):
[1] tools_3.2.2

* Out-of-date packages
                     Package               
SummarizedExperiment "SummarizedExperiment"
                     LibPath                                        Installed
SummarizedExperiment "/home/knut/R/x86_64-pc-linux-gnu-library/3.2" "1.0.0"  
                     Built   ReposVer
SummarizedExperiment "3.2.2" "1.0.1"
                     Repository                                              
SummarizedExperiment "https://bioconductor.org/packages/3.2/bioc/src/contrib"

update with biocLite()

Error: 1 package(s) out of date
ADD COMMENTlink written 24 months ago by knb0

Hi,

I can't reproduce this either. Your .libPaths() shows 2 locations: "/home/knb/R/x86_64-pc-linux-gnu-library/3.2" and "/usr/local/lib64/R/library". It could be that the same package is installed twice (once per location) but with 2 different versions. This is known to cause problems and, unfortunately, diagnostic tools like biocValid() don't report this. Please use only one installation directory if you can (delete the other one) then try to re-install GenomicRanges and run GenomicRanges:::.test() from R.

H.

ADD REPLYlink written 23 months ago by Hervé Pagès ♦♦ 13k
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