BioC experimental data: CHECK report for msdata on linux1.bioconductor.org

Package: msdata

Version: 0.8.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings msdata_0.8.0.tar.gz

StartedAt: 2015-10-24 15:09:49 -0400 (Sat, 24 Oct 2015)

EndedAt: 2015-10-24 15:10:01 -0400 (Sat, 24 Oct 2015)

EllapsedTime: 11.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: msdata.Rcheck

Warnings: 4

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings msdata_0.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-data-experiment/meat/msdata.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘msdata/DESCRIPTION’ ... OK
* this is package ‘msdata’ version ‘0.8.0’
* 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 ‘msdata’ can be installed ... [1s/1s] OK
* checking installed package size ... NOTE
  installed size is 36.2Mb
  sub-directories of 1Mb or more:
    cdf         3.5Mb
    fticr       5.8Mb
    iontrap     1.7Mb
    lockmass    4.1Mb
    microtofq  16.8Mb
    mzid        3.9Mb
* 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 ... WARNING
Found directory ‘R’ with no source files.
* 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
Error in tools:::.check_packages_used(package = "msdata") : 
  directory '/home/biocbuild/bbs-3.2-data-experiment/meat/msdata.Rcheck/msdata' does not contain R code
Execution halted
* checking S3 generic/method consistency ... WARNING
Error in tools::checkS3methods(package = "msdata") : 
  directory '/home/biocbuild/bbs-3.2-data-experiment/meat/msdata.Rcheck/msdata' does not contain R code
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error in tools::checkReplaceFuns(package = "msdata") : 
  directory '/home/biocbuild/bbs-3.2-data-experiment/meat/msdata.Rcheck/msdata' does not contain R code
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error in tools::checkFF(package = "msdata", registration = FALSE, check_DUP = TRUE) : 
  directory '/home/biocbuild/bbs-3.2-data-experiment/meat/msdata.Rcheck/msdata' does not contain R code
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking for code/documentation mismatches ... WARNING
Error in tools::codoc(package = "msdata") : 
  directory '/home/biocbuild/bbs-3.2-data-experiment/meat/msdata.Rcheck/msdata' does not contain R code
Execution halted
Error in tools::codocClasses(package = "msdata") : 
  directory '/home/biocbuild/bbs-3.2-data-experiment/meat/msdata.Rcheck/msdata' does not contain R code
Execution halted
* checking Rd \usage sections ... NOTE
Error in tools::checkDocStyle(package = "msdata") : 
  directory '/home/biocbuild/bbs-3.2-data-experiment/meat/msdata.Rcheck/msdata' does not contain R code
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [2s/2s] OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-data-experiment/meat/msdata.Rcheck/00check.log’
for details.

* installing *source* package ‘msdata’ ...
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (msdata)

name	user	system	elapsed
msdata	1.485	0.047	1.535