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CHECK report for Vega on tokay1

This page was generated on 2019-04-13 11:21:28 -0400 (Sat, 13 Apr 2019).

Package 1621/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Vega 1.30.0
Sandro Morganella
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/Vega
Branch: RELEASE_3_8
Last Commit: 2c5365a
Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Vega
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Vega.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Vega_1.30.0.tar.gz
StartedAt: 2019-04-13 06:09:09 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:10:42 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 93.2 seconds
RetCode: 0
Status:  OK  
CheckDir: Vega.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Vega.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Vega_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Vega.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Vega/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Vega' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/Vega/libs/i386/Vega.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/Vega.Rcheck/00check.log'
for details.



Installation output

Vega.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/Vega_1.30.0.tar.gz && rm -rf Vega.buildbin-libdir && mkdir Vega.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Vega.buildbin-libdir Vega_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL Vega_1.30.0.zip && rm Vega_1.30.0.tar.gz Vega_1.30.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  221k  100  221k    0     0  5130k      0 --:--:-- --:--:-- --:--:-- 5691k

install for i386

* installing *source* package 'Vega' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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;
                                                                ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Vega.dll tmp.def vega.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/Vega.buildbin-libdir/Vega/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Vega'
    finding HTML links ... done
    G519                                    html  
    Vega-package                            html  
    plotSegmentation                        html  
    vega                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Vega' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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;
                                                                ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Vega.dll tmp.def vega.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/Vega.buildbin-libdir/Vega/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Vega' as Vega_1.30.0.zip
* DONE (Vega)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'Vega' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

Vega.Rcheck/examples_i386/Vega-Ex.timings

nameusersystemelapsed
Vega-package0.210.020.39
plotSegmentation0.670.050.72
vega0.190.010.20

Vega.Rcheck/examples_x64/Vega-Ex.timings

nameusersystemelapsed
Vega-package0.180.020.21
plotSegmentation0.610.010.63
vega0.170.000.17