Package: tspair

Version: 1.38.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tspair.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings tspair_1.38.0.tar.gz

StartedAt: 2018-10-17 05:18:22 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 05:19:16 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 54.3 seconds

RetCode: 0

Status:  OK

CheckDir: tspair.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tspair.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings tspair_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/tspair.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'tspair/DESCRIPTION' ... OK
* this is package 'tspair' version '1.38.0'
* 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 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
* 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 ... 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 ... 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-3.7-bioc/R/library/tspair/libs/i386/tspair.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', 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 ...
** 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/tspair.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/tspair_1.38.0.tar.gz && rm -rf tspair.buildbin-libdir && mkdir tspair.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tspair.buildbin-libdir tspair_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL tspair_1.38.0.zip && rm tspair_1.38.0.tar.gz tspair_1.38.0.zip
###
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install for i386

* installing *source* package 'tspair' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c tsp.c -o tsp.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o tspair.dll tmp.def tsp.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/tspair.buildbin-libdir/tspair/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'tspair'
    finding HTML links ... done
    dat                                     html  
    dat2                                    html  
    eSet1                                   html  
    eSet2                                   html  
    grp                                     html  
    plot.tsp                                html  
    predict.tsp                             html  
    summary.tsp                             html  
    ts.pair                                 html  
    tspcalc                                 html  
    tspdata                                 html  
    tspplot                                 html  
    tspsig                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'tspair' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c tsp.c -o tsp.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o tspair.dll tmp.def tsp.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/tspair.buildbin-libdir/tspair/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tspair' as tspair_1.38.0.zip
* DONE (tspair)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'tspair' successfully unpacked and MD5 sums checked
In R CMD INSTALL