BioC 3.4: CHECK report for UniProt.ws on moscato1

Package: UniProt.ws

Version: 2.13.0

Command: rm -rf UniProt.ws.buildbin-libdir UniProt.ws.Rcheck && mkdir UniProt.ws.buildbin-libdir UniProt.ws.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=UniProt.ws.buildbin-libdir UniProt.ws_2.13.0.tar.gz >UniProt.ws.Rcheck\00install.out 2>&1 && cp UniProt.ws.Rcheck\00install.out UniProt.ws-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=UniProt.ws.buildbin-libdir --install="check:UniProt.ws-install.out" --force-multiarch --no-vignettes --timings UniProt.ws_2.13.0.tar.gz

StartedAt: 2016-09-20 18:02:41 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 18:12:37 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 596.3 seconds

RetCode: 0

Status:  OK

CheckDir: UniProt.ws.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf UniProt.ws.buildbin-libdir UniProt.ws.Rcheck && mkdir UniProt.ws.buildbin-libdir UniProt.ws.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=UniProt.ws.buildbin-libdir UniProt.ws_2.13.0.tar.gz >UniProt.ws.Rcheck\00install.out 2>&1 && cp UniProt.ws.Rcheck\00install.out UniProt.ws-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=UniProt.ws.buildbin-libdir --install="check:UniProt.ws-install.out" --force-multiarch --no-vignettes --timings UniProt.ws_2.13.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/UniProt.ws.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'UniProt.ws/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'UniProt.ws' version '2.13.0'
* 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 'UniProt.ws' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getSomeUniprotGoodies: no visible global function definition for
  'head'
.tryReadResult: no visible global function definition for 'read.delim'
.tryReadResult: no visible global function definition for 'URLencode'
availableUniprotSpecies: no visible global function definition for
  'read.delim'
availableUniprotSpecies: no visible global function definition for
  'head'
lookupUniprotSpeciesFromTaxId: no visible global function definition
  for 'read.delim'
Undefined global functions or variables:
  URLencode head read.delim
Consider adding
  importFrom("utils", "URLencode", "head", "read.delim")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
UniProtWS-class 8.31   2.34   61.62
colsAndKeytypes 6.15   1.50   31.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
UniProtWS-class 7.84   2.70   47.90
colsAndKeytypes 4.04   1.45   28.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'UniProt.ws_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'UniProt.ws_unit_tests.R'
 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: 1 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/UniProt.ws.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'UniProt.ws' ...
** 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 'UniProt.ws' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'UniProt.ws' as UniProt.ws_2.13.0.zip
* DONE (UniProt.ws)

name	user	system	elapsed
UniProtWS-class	8.31	2.34	61.62
colsAndKeytypes	6.15	1.50	31.52

name	user	system	elapsed
UniProtWS-class	7.84	2.70	47.90
colsAndKeytypes	4.04	1.45	28.44