[Bioc-devel] Error in .doLoadActions(where, attach) :

[Martin Morgan]

On 02/20/2014 03:44 PM, Jesper Gådin wrote:
> GenomicRanges was one version behind, but fixed that and now the biocValid()
> returns (excluding the sessionInfo)
> ....

Quite challenging. In the end you can reproduce this with

     $ cd AllelicImbalance/data
     $ R --vanilla

and then

     env = new.env()
     load("ASEset.rdata", env)
     get("ASEset", env)

The problem is with BiocParallel, and a work-around is in place in version 
0.5.14 in svn (in devel on Saturday, all being well).

Thanks for the report.

Martin

> * Packages too new for Bioconductor version '2.14'
>
>                   Version  LibPath
> AllelicImbalance "1.1.13" "/home/user/bin/R-devel/r-devel/library"
>
> downgrade with biocLite("AllelicImbalance")
>
> Error: 1 package(s) too new
>  >
>
>
> Did the rdev CMD check again, but same error as before.
>
> /Jesper
>
>
>
> On Fri, Feb 21, 2014 at 12:24 AM, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>> wrote:
>
>     On 02/20/2014 03:05 PM, Jesper Gådin wrote:
>
>         Hi all,
>
>         Tried to R CMD build and check the AllelicImbalance package, but got a
>         strange NOTE during R CMD check (see below). Have checked previous versions
>         of AllelicImbalance to try to find when the NOTE/Error got introduced, but
>         the R CMD check on the old build files gives the same response. And I
>         am certain that this NOTE did not occur earlier in these other versions. So
>         probably another package like e.g. GenomicAlignments or BiocParallell has
>         changed in some way that affects AllelicImbalance to throw this NOTE/error.
>
>         Any suggestions?
>
>         /Jesper
>
>             rdev CMD check AllelicImbalance_1.1.13.tar.gz
>
>
>         ....
>         * checking for unstated dependencies in examples ... OK
>         * checking contents of 'data' directory ... OK
>         * checking data for non-ASCII characters ... NOTE
>             Error in .doLoadActions(where, attach) :
>               error in load action .__A__.registerDefaultParams for package
>         BiocParallel: initialize(value, ...): attempt to apply non-function
>             Failed with error:  'package 'GenomicAlignments' could not be loaded'
>
>
>     Is GenomicAlignments (and other?) current?
>
>          biocValid()
>
>
>             Error in .requirePackage(package) :
>               unable to find required package 'AllelicImbalance'
>             Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef
>         -> .requirePackage
>             Execution halted
>         * checking data for ASCII and uncompressed saves ... OK
>         * checking installed files from 'inst/doc' ... OK
>         * checking files in 'vignettes' ... OK
>         * checking examples ... OK
>         * checking for unstated dependencies in tests ... OK
>         * checking tests ...
>             Running 'runTests.R'
>            OK
>         * checking for unstated dependencies in vignettes ... OK
>         * checking package vignettes in 'inst/doc' ... OK
>         * checking running R code from vignettes ...
>              'AllelicImbalance.Rnw' using 'UTF-8' ... OK
>            OK
>         * checking re-building of vignette outputs ... OK
>         * checking PDF version of manual ... OK
>
>         NOTE: There was 1 note.
>         See
>         .....
>
>
>
>             sessionInfo()
>
>         R Under development (unstable) (2013-11-13 r64209)
>         Platform: x86_64-unknown-linux-gnu (64-bit)
>
>         locale:
>            [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>            [3] 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
>            [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>            [9] LC_ADDRESS=C               LC_TELEPHONE=C
>         [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>         attached base packages:
>         [1] parallel  stats     graphics  grDevices utils     datasets  methods
>         [8] base
>
>         other attached packages:
>         [1] AllelicImbalance_1.1.13   GenomicAlignments_0.99.23
>         [3] Rsamtools_1.15.28         Biostrings_2.31.13
>         [5] XVector_0.3.7             GenomicRanges_1.15.30
>         [7] IRanges_1.21.31           BiocGenerics_0.9.3
>
>         loaded via a namespace (and not attached):
>            [1] AnnotationDbi_1.25.9   BatchJobs_1.2          BBmisc_1.5
>            [4] Biobase_2.23.4         BiocParallel_0.5.8     biomaRt_2.19.3
>            [7] bitops_1.0-6           brew_1.0-6             BSgenome_1.31.11
>         [10] codetools_0.2-8        DBI_0.2-7              digest_0.6.4
>         [13] fail_1.2               foreach_1.4.1          GenomicFeatures_1.15.6
>         [16] iterators_1.0.6        plyr_1.8               RCurl_1.95-4.1
>         [19] RSQLite_0.11.4         rtracklayer_1.23.12    sendmailR_1.1-2
>         [22] stats4_3.1.0           stringr_0.6.2          tools_3.1.0
>         [25] XML_3.98-1.1           zlibbioc_1.9.0
>
>
>
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Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793