BioC 3.2: CHECK report for SNAGEE on moscato1

Package: SNAGEE

Version: 1.9.0

Command: rm -rf SNAGEE.buildbin-libdir SNAGEE.Rcheck && mkdir SNAGEE.buildbin-libdir SNAGEE.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SNAGEE.buildbin-libdir SNAGEE_1.9.0.tar.gz >SNAGEE.Rcheck\00install.out 2>&1 && cp SNAGEE.Rcheck\00install.out SNAGEE-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=SNAGEE.buildbin-libdir --install="check:SNAGEE-install.out" --force-multiarch --no-vignettes --timings SNAGEE_1.9.0.tar.gz

StartedAt: 2015-08-20 10:32:33 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 10:34:26 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 113.5 seconds

RetCode: 0

Status:  OK

CheckDir: SNAGEE.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf SNAGEE.buildbin-libdir SNAGEE.Rcheck && mkdir SNAGEE.buildbin-libdir SNAGEE.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SNAGEE.buildbin-libdir SNAGEE_1.9.0.tar.gz >SNAGEE.Rcheck\00install.out 2>&1 && cp SNAGEE.Rcheck\00install.out SNAGEE-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=SNAGEE.buildbin-libdir --install="check:SNAGEE-install.out" --force-multiarch --no-vignettes --timings SNAGEE_1.9.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/SNAGEE.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SNAGEE/DESCRIPTION' ... OK
* this is package 'SNAGEE' version '1.9.0'
* 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 'SNAGEE' 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
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
qualSample: no visible global function definition for 'mclapply'
toSnageeFormat: no visible global function definition for 'annotation'
toSnageeFormat: no visible global function definition for 'exprs'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [45s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
SNAGEE-package 16.87   3.11   21.46
qualSample     11.69   3.26   14.95
** running examples for arch 'x64' ... [45s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
SNAGEE-package 17.1   3.51   20.60
qualSample     13.6   3.17   16.77
* 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
  'D:/biocbld/bbs-3.2-bioc/meat/SNAGEE.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'SNAGEE' ...
** R
** 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 'SNAGEE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SNAGEE' as SNAGEE_1.9.0.zip
* DONE (SNAGEE)

name	user	system	elapsed
SNAGEE-package	16.87	3.11	21.46
qualSample	11.69	3.26	14.95
qualStudy	3.52	0.09	3.62
toSnageeFormat	3.90	0.02	3.91

name	user	system	elapsed
SNAGEE-package	17.10	3.51	20.60
qualSample	13.60	3.17	16.77
qualStudy	3.45	0.06	3.51
toSnageeFormat	3.24	0.10	3.34