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

[Martin Morgan]

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
>>
>
> 	[[alternative HTML version deleted]]
>
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