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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