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BioC 3.3: CHECK report for clonotypeR on zin2

This page was generated on 2016-10-13 12:43:55 -0700 (Thu, 13 Oct 2016).

Package 199/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clonotypeR 1.10.2
Charles Plessy
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/clonotypeR
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clonotypeR
Version: 1.10.2
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings clonotypeR_1.10.2.tar.gz
StartedAt: 2016-10-13 00:36:23 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 00:36:37 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 14.4 seconds
RetCode: 0
Status:  OK 
CheckDir: clonotypeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings clonotypeR_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/clonotypeR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clonotypeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clonotypeR’ version ‘1.10.2’
* 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 ‘clonotypeR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking 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 ... NOTE
clonotype_table: no visible global function definition for ‘reshape’
read_clonotypes: no visible global function definition for ‘read.table’
yassai_identifier,ANY-missing-missing-ANY: no visible global function
  definition for ‘read.table’
yassai_identifier,data.frame-data.frame-data.frame-logical: no visible
  global function definition for ‘read.table’
Undefined global functions or variables:
  read.table reshape
Consider adding
  importFrom("stats", "reshape")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/clonotypeR.Rcheck/00check.log’
for details.


clonotypeR.Rcheck/00install.out:

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

clonotypeR.Rcheck/clonotypeR-Ex.timings:

nameusersystemelapsed
clonotype_table0.0260.0000.026
clonotyper_extdata0.0050.0000.005
common_clonotypes0.0260.0000.026
is_unproductive0.0000.0000.004
private_clonotypes0.0140.0000.014
read_clonotypes0.0040.0000.004
unique_clonotypes0.0160.0000.016
yassai_identifier0.1320.0000.132