BioC 2.13: CHECK report for STRINGdb on moscato1

Package: STRINGdb

Version: 1.0.1

Command: rm -rf STRINGdb.buildbin-libdir && mkdir STRINGdb.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=STRINGdb.buildbin-libdir STRINGdb_1.0.1.tar.gz >STRINGdb-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=STRINGdb.buildbin-libdir --install="check:STRINGdb-install.out" --force-multiarch --no-vignettes --timings STRINGdb_1.0.1.tar.gz && mv STRINGdb.buildbin-libdir/* STRINGdb.Rcheck/ && rmdir STRINGdb.buildbin-libdir

StartedAt: 2014-04-05 07:04:44 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 07:30:02 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 1518.4 seconds

RetCode: 0

Status:  OK

CheckDir: STRINGdb.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/STRINGdb.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'STRINGdb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'STRINGdb' version '1.0.1'
* 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 'STRINGdb' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
* 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
Packages in Depends field not imported from:
  'RCurl' 'igraph' 'methods' 'plotrix' 'plyr' 'png' 'sqldf'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_STRING_species: no visible binding for global variable
  'official_name'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'STRINGdb.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [478s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
STRINGdb-package 166.46   2.14  269.04
STRINGdb         136.65   1.08  205.61
** running examples for arch 'x64' ... [586s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
STRINGdb-package 185.86   2.57  360.21
STRINGdb         132.23   1.45  222.53
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [189s]
 [190s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [183s]
 [184s] 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/STRINGdb.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'STRINGdb' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'STRINGdb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'STRINGdb' as STRINGdb_1.0.1.zip
* DONE (STRINGdb)

name	user	system	elapsed
STRINGdb-class	0	0	0
STRINGdb-package	166.46	2.14	269.04
STRINGdb	136.65	1.08	205.61

name	user	system	elapsed
STRINGdb-class	0.02	0.00	0.02
STRINGdb-package	185.86	2.57	360.21
STRINGdb	132.23	1.45	222.53