RnBeads.hg19 1.2.1
RnBeadsAnnotationCreator
| Snapshot Date: 2016-04-20 09:20:20 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_2/experiment/pkgs/RnBeads.hg19 | | Last Changed Rev: 3605 / Revision: 3730 | | Last Changed Date: 2016-02-22 09:55:15 -0800 (Mon, 22 Feb 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RnBeads.hg19_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-data-experiment/meat/RnBeads.hg19.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnBeads.hg19/DESCRIPTION’ ... OK
* this is package ‘RnBeads.hg19’ version ‘1.2.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RnBeads.hg19’ can be installed ... [6s/7s] OK
* checking installed package size ... NOTE
installed size is 136.8Mb
sub-directories of 1Mb or more:
data 136.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘GenomicRanges’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
‘rnb.set.example’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
Error : .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
call: initialize(value, ...)
error: attempt to apply non-function
Failed with error: 'package 'TxDb.Hsapiens.UCSC.hg19.knownGene' could not be loaded'
Error in .requirePackage(package) :
unable to find required package 'RnBeads'
Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
Execution halted
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
CpG.RData 102.6Mb 67.0Mb xz
probes27.RData 749Kb 493Kb xz
probes450.RData 9.7Mb 6.3Mb xz
probesEPIC.RData 14.6Mb 10.7Mb xz
regions.RData 8.6Mb 4.2Mb xz
small.example.object.RData 508Kb 365Kb xz
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.2-data-experiment/meat/RnBeads.hg19.Rcheck/00check.log’
for details.