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BioC 3.5: CHECK report for tspair on malbec2

This page was generated on 2017-08-16 13:13:17 -0400 (Wed, 16 Aug 2017).

Package 1339/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tspair 1.34.0
Jeffrey T. Leek
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/tspair
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: tspair
Version: 1.34.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings tspair_1.34.0.tar.gz
StartedAt: 2017-08-16 02:47:13 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:47:37 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 23.8 seconds
RetCode: 0
Status:  OK 
CheckDir: tspair.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings tspair_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/tspair.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tspair/DESCRIPTION’ ... OK
* this is package ‘tspair’ version ‘1.34.0’
* 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 ‘tspair’ 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘Biobase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
predict.tsp: no visible global function definition for ‘featureNames’
predict.tsp: no visible global function definition for ‘exprs’
tspcalc: no visible global function definition for ‘exprs’
tspcalc: no visible global function definition for ‘featureNames’
tspcalc: no visible global function definition for ‘pData’
tspplot: no visible global function definition for ‘par’
tspplot: no visible global function definition for ‘plot’
tspplot: no visible global function definition for ‘points’
tspplot: no visible global function definition for ‘abline’
tspplot: no visible global function definition for ‘mtext’
tspsig: no visible global function definition for ‘pData’
tspsig: no visible global function definition for ‘exprs’
tspsig: no visible global function definition for ‘txtProgressBar’
tspsig: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  abline exprs featureNames mtext pData par plot points
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "mtext", "par", "plot", "points")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/tspair.Rcheck/00check.log’
for details.


tspair.Rcheck/00install.out:

* installing *source* package ‘tspair’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c tsp.c -o tsp.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o tspair.so tsp.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/tspair.Rcheck/tspair/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (tspair)

tspair.Rcheck/tspair-Ex.timings:

nameusersystemelapsed
plot.tsp0.0000.0040.001
predict.tsp000
summary.tsp0.0000.0000.001
ts.pair0.0000.0000.001
tspcalc0.0000.0000.001
tspplot000
tspsig000