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CHECK report for Vega on malbec2

This page was generated on 2018-10-17 08:23:22 -0400 (Wed, 17 Oct 2018).

Package 1535/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Vega 1.28.0
Sandro Morganella
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Vega
Branch: RELEASE_3_7
Last Commit: 1fd439c
Last Changed Date: 2018-04-30 10:35:15 -0400 (Mon, 30 Apr 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Vega
Version: 1.28.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:Vega.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings Vega_1.28.0.tar.gz
StartedAt: 2018-10-16 04:24:39 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 04:24:55 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 15.5 seconds
RetCode: 0
Status:  OK 
CheckDir: Vega.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:Vega.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings Vega_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/Vega.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Vega/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Vega’ version ‘1.28.0’
* 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 ‘Vega’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotSegmentation: no visible global function definition for ‘par’
plotSegmentation: no visible global function definition for ‘plot’
plotSegmentation: no visible global function definition for ‘lines’
vega: no visible global function definition for ‘sd’
vega: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines par plot sd write.table
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "sd")
  importFrom("utils", "write.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 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
* 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-3.7-bioc/meat/Vega.Rcheck/00check.log’
for details.



Installation output

Vega.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL Vega
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘Vega’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c vega.c -o vega.o
vega.c: In function ‘heap_delete’:
vega.c:201:8: warning: variable ‘deleted’ set but not used [-Wunused-but-set-variable]
   node deleted;
        ^
vega.c: In function ‘vega’:
vega.c:355:13: warning: unused variable ‘maxptr’ [-Wunused-variable]
  node max, *maxptr, tmp_node;
             ^
vega.c:348:68: warning: unused variable ‘tmp_lambda2’ [-Wunused-variable]
  double lambda, lambda_gradient, stop_lambda_gradient, tmp_lambda, tmp_lambda2;
                                                                    ^
vega.c:347:6: warning: unused variable ‘index’ [-Wunused-variable]
  int index;
      ^
vega.c: In function ‘update_priority’:
vega.c:560:64: warning: unused variable ‘next_mean’ [-Wunused-variable]
  double lambda, first_term, second_term, prev_mean, curr_mean, next_mean;
                                                                ^
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o Vega.so vega.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/Vega/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
* DONE (Vega)

Tests output


Example timings

Vega.Rcheck/Vega-Ex.timings

nameusersystemelapsed
Vega-package0.2040.0040.206
plotSegmentation0.5080.0240.530
vega0.1680.0000.167