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 <mtmor...@fhcrc.org
<mailto:mtmor...@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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