GenomicRanges was one version behind, but fixed that and now the
biocValid() returns (excluding the sessionInfo)
....
* 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@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
>>
>>>
>>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
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>
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