BioC experimental data: CHECK report for RNAseqData.HeLa.bam.chr14 on petty

Package: RNAseqData.HeLa.bam.chr14

Version: 0.1.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAseqData.HeLa.bam.chr14_0.1.4.tar.gz

StartedAt: 2013-10-08 14:24:22 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 14:27:33 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 191.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RNAseqData.HeLa.bam.chr14.Rcheck

Warnings: 3

* using log directory '/Users/biocbuild/bbs-2.12-data-experiment/meat/RNAseqData.HeLa.bam.chr14.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RNAseqData.HeLa.bam.chr14/DESCRIPTION' ... OK
* this is package 'RNAseqData.HeLa.bam.chr14' version '0.1.4'
* 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.HeLa.bam.chr14' can be installed ... [1s/1s] WARNING
Found the following significant warnings:
  Warning: 
See '/Users/biocbuild/bbs-2.12-data-experiment/meat/RNAseqData.HeLa.bam.chr14.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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 '/Users/biocbuild/bbs-2.12-data-experiment/meat/RNAseqData.HeLa.bam.chr14.Rcheck/00_pkg_src/RNAseqData.HeLa.bam.chr14/man/RNAseqData.HeLa.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 ... WARNING
'::' or ':::' import not declared from: 'BiocInstaller'
'library' or 'require' call not declared from: 'Rsamtools'
* checking examples ... [35s/35s] OK
Examples with CPU or elapsed time > 5s
                                    user system elapsed
RNAseqData.HeLa.bam.chr14-package 31.552  2.822  34.425
* checking PDF version of manual ... OK

WARNING: There were 3 warnings.
See
  '/Users/biocbuild/bbs-2.12-data-experiment/meat/RNAseqData.HeLa.bam.chr14.Rcheck/00check.log'
for details.

* installing *source* package 'RNAseqData.HeLa.bam.chr14' ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: 
                    * * * * * * * * * * * * * * * * * * * *
 The RNAseqData.HeLa.bam.chr14 package was renamed RNAseqData.HNRNPC.bam.chr14.
        RNAseqData.HeLa.bam.chr14 is still available but is DEPRECATED.
          Please use the RNAseqData.HNRNPC.bam.chr14 package instead.
                    * * * * * * * * * * * * * * * * * * * *
* DONE (RNAseqData.HeLa.bam.chr14)

name	user	system	elapsed
RNAseqData.HeLa.bam.chr14-package	31.552	2.822	34.425