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BioC experimental data: CHECK report for SpikeIn on malbec1

This page was generated on 2017-04-15 16:49:28 -0400 (Sat, 15 Apr 2017).

Package 281/310HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpikeIn 1.16.0
Rafael A. Irizarry
Snapshot Date: 2017-04-15 09:20:05 -0400 (Sat, 15 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_4/experiment/pkgs/SpikeIn
Last Changed Rev: 3958 / Revision: 4141
Last Changed Date: 2016-10-17 14:47:53 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository

Summary

Package: SpikeIn
Version: 1.16.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SpikeIn_1.16.0.tar.gz
StartedAt: 2017-04-15 11:21:15 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 11:21:44 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 29.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: SpikeIn.Rcheck
Warnings: 5

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SpikeIn_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/SpikeIn.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpikeIn/DESCRIPTION’ ... OK
* this is package ‘SpikeIn’ version ‘1.16.0’
* 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 ‘SpikeIn’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 63.1Mb
  sub-directories of 1Mb or more:
    data  63.0Mb
* 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 = "SpikeIn") : 
  directory '/home/biocbuild/bbs-3.4-data-experiment/meat/SpikeIn.Rcheck/SpikeIn' does not contain R code
Execution halted
* checking S3 generic/method consistency ... WARNING
Error in tools::checkS3methods(package = "SpikeIn") : 
  directory '/home/biocbuild/bbs-3.4-data-experiment/meat/SpikeIn.Rcheck/SpikeIn' 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 = "SpikeIn") : 
  directory '/home/biocbuild/bbs-3.4-data-experiment/meat/SpikeIn.Rcheck/SpikeIn' 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 = "SpikeIn", registration = FALSE, check_DUP = TRUE) : 
  directory '/home/biocbuild/bbs-3.4-data-experiment/meat/SpikeIn.Rcheck/SpikeIn' 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 = "SpikeIn") : 
  directory '/home/biocbuild/bbs-3.4-data-experiment/meat/SpikeIn.Rcheck/SpikeIn' does not contain R code
Execution halted
Error in tools::codocClasses(package = "SpikeIn") : 
  directory '/home/biocbuild/bbs-3.4-data-experiment/meat/SpikeIn.Rcheck/SpikeIn' does not contain R code
Execution halted
* checking Rd \usage sections ... NOTE
Error in tools::checkDocStyle(package = "SpikeIn") : 
  directory '/home/biocbuild/bbs-3.4-data-experiment/meat/SpikeIn.Rcheck/SpikeIn' 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: package needs dependence on R (>= 2.10)
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-data-experiment/meat/SpikeIn.Rcheck/00check.log’
for details.


SpikeIn.Rcheck/00install.out:

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