BioC experimental data: CHECK report for RNAseqData.HNRNPC.bam.chr14 on george2

Package: RNAseqData.HNRNPC.bam.chr14

Version: 0.1.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RNAseqData.HNRNPC.bam.chr14_0.1.3.tar.gz

StartedAt: 2013-10-08 13:13:26 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 13:15:46 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 139.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RNAseqData.HNRNPC.bam.chr14.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.12-data-experiment/meat/RNAseqData.HNRNPC.bam.chr14.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAseqData.HNRNPC.bam.chr14/DESCRIPTION’ ... OK
* this is package ‘RNAseqData.HNRNPC.bam.chr14’ version ‘0.1.3’
* 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 ‘RNAseqData.HNRNPC.bam.chr14’ can be installed ... [3s/6s] OK
* checking installed package size ... NOTE
  installed size is 420.3Mb
  sub-directories of 1Mb or more:
    extdata  420.1Mb
* 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 for unstated dependencies in R code ... OK
* 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 ... WARNING
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-data-experiment/meat/RNAseqData.HNRNPC.bam.chr14.Rcheck/00_pkg_src/RNAseqData.HNRNPC.bam.chr14/man/RNAseqData.HNRNPC.bam.chr14-package.Rd’:
  ‘[GenomicRanges]{readGAlignmentPairs}’

See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [60s/62s] OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
RNAseqData.HNRNPC.bam.chr14-package 58.491  0.628  61.403
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-data-experiment/meat/RNAseqData.HNRNPC.bam.chr14.Rcheck/00check.log’
for details.

* installing *source* package ‘RNAseqData.HNRNPC.bam.chr14’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (RNAseqData.HNRNPC.bam.chr14)

name	user	system	elapsed
RNAseqData.HNRNPC.bam.chr14-package	58.491	0.628	61.403