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BioC experimental data: CHECK report for yeastCC on petty

This page was generated on 2015-10-07 16:21:35 -0700 (Wed, 07 Oct 2015).

Package 235/241HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
yeastCC 1.8.0
Sandrine Dudoit
Snapshot Date: 2015-10-07 07:15:35 -0700 (Wed, 07 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs/yeastCC
Last Changed Rev: 3279 / Revision: 3442
Last Changed Date: 2015-04-16 13:16:53 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: yeastCC
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings yeastCC_1.8.0.tar.gz
StartedAt: 2015-10-07 10:02:45 -0700 (Wed, 07 Oct 2015)
EndedAt: 2015-10-07 10:03:34 -0700 (Wed, 07 Oct 2015)
EllapsedTime: 48.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: yeastCC.Rcheck
Warnings: 5

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings yeastCC_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-data-experiment/meat/yeastCC.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yeastCC/DESCRIPTION’ ... OK
* this is package ‘yeastCC’ version ‘1.8.0’
* 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 ‘yeastCC’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 = "yeastCC") : 
  directory '/Users/biocbuild/bbs-3.1-data-experiment/meat/yeastCC.Rcheck/yeastCC' does not contain R code
Execution halted
* checking S3 generic/method consistency ... WARNING
Error in tools::checkS3methods(package = "yeastCC") : 
  directory '/Users/biocbuild/bbs-3.1-data-experiment/meat/yeastCC.Rcheck/yeastCC' 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 = "yeastCC") : 
  directory '/Users/biocbuild/bbs-3.1-data-experiment/meat/yeastCC.Rcheck/yeastCC' 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 = "yeastCC", registration = FALSE, check_DUP = TRUE) : 
  directory '/Users/biocbuild/bbs-3.1-data-experiment/meat/yeastCC.Rcheck/yeastCC' 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 = "yeastCC") : 
  directory '/Users/biocbuild/bbs-3.1-data-experiment/meat/yeastCC.Rcheck/yeastCC' does not contain R code
Execution halted
Error in tools::codocClasses(package = "yeastCC") : 
  directory '/Users/biocbuild/bbs-3.1-data-experiment/meat/yeastCC.Rcheck/yeastCC' does not contain R code
Execution halted
* checking Rd \usage sections ... NOTE
Error in tools::checkDocStyle(package = "yeastCC") : 
  directory '/Users/biocbuild/bbs-3.1-data-experiment/meat/yeastCC.Rcheck/yeastCC' 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 ... WARNING
  Warning: large data file saved inefficiently:
                 size ASCII compress
  spYCCmeta.rda 430Kb FALSE     none
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                old_size new_size compress
  breeden.rda      1.9Mb    1.5Mb       xz
  spYCCES.rda      757Kb    483Kb       xz
  spYCCmeta.rda    430Kb     55Kb       xz
  yeastCC.rda      1.5Mb    485Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] OK
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-data-experiment/meat/yeastCC.Rcheck/00check.log’
for details.


yeastCC.Rcheck/00install.out:

* installing *source* package ‘yeastCC’ ...
** data
*** moving datasets to lazyload DB
** inst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (yeastCC)

yeastCC.Rcheck/yeastCC-Ex.timings:

nameusersystemelapsed
breeden0.1470.0160.163
orf8000.0020.0000.002
spYCCmeta0.0170.0010.018
yeastCC0.2270.0130.240