Package: ChemmineR

Version: 2.10.9

Command: rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChemmineR.buildbin-libdir ChemmineR_2.10.9.tar.gz >ChemmineR-install.out 2>&1 && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD check --library=ChemmineR.buildbin-libdir --install="check:ChemmineR-install.out" --force-multiarch --no-vignettes --timings ChemmineR_2.10.9.tar.gz && mv ChemmineR.buildbin-libdir/* ChemmineR.Rcheck/ && rmdir ChemmineR.buildbin-libdir

StartedAt: 2013-03-25 00:17:42 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:21:48 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 246.2 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/ChemmineR.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChemmineR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineR' version '2.10.9'
* 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 whether package 'ChemmineR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 for unstated 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
Found the following possibly unsafe calls:
File 'R/sim.R':
  found unlockBinding(".progress_bar_int_cnt",
    environment(.progress_bar))
.data.frame.to.str: no visible binding for global variable 'string'
.gen_atom_pair: no visible global function definition for
  'Descriptors_get_len'
.gen_atom_pair: no visible global function definition for
  'Descriptors_get_descriptor'
.parse: no visible global function definition for 'Descriptors'
.parse: no visible global function definition for
  'Descriptors_parse_sdf'
cmp.parse: no visible global function definition for 'batch_parse'
cmp.parse1: no visible global function definition for
  'delete_Descriptors'
datablock2ma: no visible binding for global variable 'sdfset'
sdf_to_desc: no visible global function definition for
  'delete_Descriptors'
sdfs_to_desc: no visible global function definition for 'batch_parse'
* 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
sdf2ap       13.46   0.01   13.47
AP-class     13.04   0.05   13.11
APset-class  12.48   0.03   12.51
apset2descdb 12.34   0.04   12.37
ap           12.00   0.03   12.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
AP-class     12.79   0.06   12.87
ap           11.67   0.02   11.68
APset-class  11.66   0.01   11.67
sdf2ap       11.47   0.02   11.48
apset2descdb 11.44   0.03   11.47
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  'fmcsR' 'gplots' 'scatterplot3d'
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-2.11-bioc/meat/ChemmineR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ChemmineR' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'as.vector' from package 'base' in package 'ChemmineR'
Creating a generic function for 'as.matrix' from package 'base' in package 'ChemmineR'
Creating a generic function for 'plot' from package 'graphics' in package 'ChemmineR'
** help
*** installing help indices
** building package indices
** installing vignettes
   'ChemmineR.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'ChemmineR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChemmineR' as ChemmineR_2.10.9.zip

* DONE (ChemmineR)