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CHECK report for tspair on malbec2

This page was generated on 2020-10-17 11:55:58 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE tspair PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1843/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tspair 1.46.0
Jeffrey T. Leek
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/tspair
Branch: RELEASE_3_11
Last Commit: 432207a
Last Changed Date: 2020-04-27 14:18:50 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: tspair
Version: 1.46.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:tspair.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings tspair_1.46.0.tar.gz
StartedAt: 2020-10-17 06:16:00 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:16:30 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 30.5 seconds
RetCode: 0
Status:  OK 
CheckDir: tspair.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:tspair.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings tspair_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/tspair.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.46.0’
* 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 ‘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 points setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "mtext", "par", "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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.11-bioc/R/library/tspair/libs/tspair.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/tspair.Rcheck/00check.log’
for details.



Installation output

tspair.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL tspair
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘tspair’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c tsp.c -o tsp.o
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o tspair.so tsp.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-tspair/00new/tspair/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tspair)

Tests output


Example timings

tspair.Rcheck/tspair-Ex.timings

nameusersystemelapsed
plot.tsp000
predict.tsp0.0000.0000.001
summary.tsp000
ts.pair0.0000.0000.001
tspcalc000
tspplot0.0010.0000.000
tspsig000