BioC 2.13: CHECK report for rTRM on moscato1

Package: rTRM

Version: 1.0.5

Command: rm -rf rTRM.buildbin-libdir && mkdir rTRM.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rTRM.buildbin-libdir rTRM_1.0.5.tar.gz >rTRM-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=rTRM.buildbin-libdir --install="check:rTRM-install.out" --force-multiarch --no-vignettes --timings rTRM_1.0.5.tar.gz && mv rTRM.buildbin-libdir/* rTRM.Rcheck/ && rmdir rTRM.buildbin-libdir

StartedAt: 2014-04-05 06:36:51 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 06:39:29 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 158.2 seconds

RetCode: 0

Status:  OK

CheckDir: rTRM.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/rTRM.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 'rTRM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rTRM' version '1.0.5'
* 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 'rTRM' 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
Packages in Depends field not imported from:
  'RSQLite' 'annotate' 'igraph'
  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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [8s] OK
** running examples for arch 'x64' ... [12s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
getMatrices 6.14      0    6.15
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [5s]
 [5s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [6s]
 [7s] 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 was 1 note.
See
  'D:/biocbld/bbs-2.13-bioc/meat/rTRM.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'rTRM' ...
** R
** data
** inst
** byte-compile and prepare 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 'rTRM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rTRM' as rTRM_1.0.5.zip
* DONE (rTRM)

name	user	system	elapsed
findTRM	0.20	0.00	0.21
getAnnotations	0.01	0.00	0.02
getMaps	0.06	0.00	0.06
getMatrices	2.7	0.0	2.7
getOrthologs	0.01	0.02	0.03
rTRM-package	0.07	0.00	0.07

name	user	system	elapsed
findTRM	0.25	0.00	0.25
getAnnotations	0.03	0.00	0.03
getMaps	0.05	0.02	0.07
getMatrices	6.14	0.00	6.15
getOrthologs	0.02	0.01	0.03
rTRM-package	0.06	0.00	0.07