Problem installing XVector package
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gary_smith • 0
@gary_smith-11234
Last seen 5.1 years ago

I'm trying to install biocLite(gcrma) and it appears to be hanging up on the Xvector & IRanges build.  Can anyone give me a clue about this matchSignature() error?

 

** R

** inst

** preparing package for lazy loading

Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’

Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’

in method for ‘coerce’ with signature ‘"Hits","PartitioningByEnd"’: no definition for class “PartitioningByEnd”

in method for ‘coerce’ with signature ‘"Hits","Partitioning"’: no definition for class “Partitioning”

in method for ‘coerce’ with signature ‘"Hits","Ranges"’: no definition for class “Ranges”

in method for ‘coerce’ with signature ‘"Hits","IRanges"’: no definition for class “IRanges”

in method for ‘coerce’ with signature ‘"Hits","CompressedIntegerList"’: no definition for class “CompressedIntegerList”

in method for ‘coerce’ with signature ‘"Hits","IntegerList"’: no definition for class “IntegerList”

Creating a generic function for ‘stack’ from package ‘utils’ in package ‘IRanges’

Creating a generic function for ‘compare’ from package ‘S4Vectors’ in package ‘IRanges’

Error in matchSignature(signature, fdef) : 

  more elements in the method signature (2) than in the generic signature (1) for function ‘compare’

Error : unable to load R code in package ‘IRanges’

ERROR: lazy loading failed for package ‘IRanges’

* removing ‘/cluster/app/R-3.2.4/lib64/R/library/IRanges’

* restoring previous ‘/cluster/app/R-3.2.4/lib64/R/library/IRanges’

 

The downloaded source packages are in

    ‘/tmp/RtmpQSmiLd/downloaded_packages’

Updating HTML index of packages in '.Library'

Making 'packages.html' ... done

software error gcrma Xvector iranges • 1.3k views
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Does BiocInstaller::biocValid() report out-of-date or otherwise incorrect package versions?

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yes, you got it.  What does "too new" mean?

* Out-of-date packages

[------>8----snip---->8------]

update with biocLite()

 

* Packages too new for Bioconductor version '3.2'

 

              Version  LibPath                               

AnnotationDbi "1.33.7" "/cluster/app/R-3.2.4/lib64/R/library"

Biobase       "2.31.3" "/cluster/app/R-3.2.4/lib64/R/library"

BiocGenerics  "0.17.3" "/cluster/app/R-3.2.4/lib64/R/library"

GenomeInfoDb  "1.7.6"  "/cluster/app/R-3.2.4/lib64/R/library"

graph         "1.49.1" "/cluster/app/R-3.2.4/lib64/R/library"

IRanges       "2.5.40" "/cluster/app/R-3.2.4/lib64/R/library"

Rgraphviz     "2.15.0" "/cluster/app/R-3.2.4/lib64/R/library"

S4Vectors     "0.9.44" "/cluster/app/R-3.2.4/lib64/R/library"

 

downgrade with biocLite(c("AnnotationDbi", "Biobase", "BiocGenerics", "GenomeInfoDb", "graph",

  "IRanges", "Rgraphviz", "S4Vectors"))

 

Error: 26 package(s) out of date; 8 package(s) too new

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These look like 'devel' packages (odd number in the 'y' position of x.y.z); likely packages from the 'devel' branch were installed in the same location as the 'release' branch.

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gary_smith • 0
@gary_smith-11234
Last seen 5.1 years ago

 

* installing *source* package ‘RcppArmadillo’ ...

** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked

checking whether the C++ compiler works... yes

checking for C++ compiler default output file name... a.out

checking for suffix of executables... 

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C++ compiler... yes

checking whether g++ accepts -g... yes

checking how to run the C++ preprocessor... g++ -E

checking whether we are using the GNU C++ compiler... (cached) yes

checking whether g++ accepts -g... (cached) yes

checking whether g++ version is sufficient... no

configure: WARNING: Only g++ version 4.6 or greater can be used with RcppArmadillo.

configure: error: Please use a different compiler.

ERROR: configuration failed for package ‘RcppArmadillo’

* removing ‘/cluster/app/R-3.2.4/lib64/R/library/RcppArmadillo’

* restoring previous ‘/cluster/app/R-3.2.4/lib64/R/library/RcppArmadillo’

 

The downloaded source packages are in

    ‘/tmp/RtmpwYGZs4/downloaded_packages’

Updating HTML index of packages in '.Library'

Making 'packages.html' ... done

Warning message:

In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :

  installation of package ‘RcppArmadillo’ had non-zero exit status

After correcting some of the out of date packages, I'm now stuck on Rgraphviz and RcppArmadillo.  Neither will build under RHEL6.8 because they want a GCC 4.6 compiler.  That seems a bit extreme.

 

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I guess RcppArmadillo is 'not our problem' (in the sense that we can't do anything about it, other than feel your pain...), the package CRAN landing page points to appropriate help resources; the 'Old sources' link points to previous versions which presumably did not have this requirement, and can be installed with install.pacakages(url-to-version.tar.gz, repos=NULL). What's the issue with Rgraphviz? Also, I think the 

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