BioC 3.3: CHECK report for ProteomicsAnnotationHubData on moscato2

Package: ProteomicsAnnotationHubData

Version: 1.2.2

Command: rm -rf ProteomicsAnnotationHubData.buildbin-libdir ProteomicsAnnotationHubData.Rcheck && mkdir ProteomicsAnnotationHubData.buildbin-libdir ProteomicsAnnotationHubData.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProteomicsAnnotationHubData.buildbin-libdir ProteomicsAnnotationHubData_1.2.2.tar.gz >ProteomicsAnnotationHubData.Rcheck\00install.out 2>&1 && cp ProteomicsAnnotationHubData.Rcheck\00install.out ProteomicsAnnotationHubData-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ProteomicsAnnotationHubData.buildbin-libdir --install="check:ProteomicsAnnotationHubData-install.out" --force-multiarch --no-vignettes --timings ProteomicsAnnotationHubData_1.2.2.tar.gz

StartedAt: 2016-10-13 07:35:19 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:42:47 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 447.2 seconds

RetCode: 0

Status:  OK

CheckDir: ProteomicsAnnotationHubData.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ProteomicsAnnotationHubData.buildbin-libdir ProteomicsAnnotationHubData.Rcheck && mkdir ProteomicsAnnotationHubData.buildbin-libdir ProteomicsAnnotationHubData.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProteomicsAnnotationHubData.buildbin-libdir ProteomicsAnnotationHubData_1.2.2.tar.gz >ProteomicsAnnotationHubData.Rcheck\00install.out 2>&1 && cp ProteomicsAnnotationHubData.Rcheck\00install.out ProteomicsAnnotationHubData-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ProteomicsAnnotationHubData.buildbin-libdir --install="check:ProteomicsAnnotationHubData-install.out" --force-multiarch --no-vignettes --timings ProteomicsAnnotationHubData_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/ProteomicsAnnotationHubData.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 'ProteomicsAnnotationHubData/DESCRIPTION' ... OK
* this is package 'ProteomicsAnnotationHubData' version '1.2.2'
* 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 'ProteomicsAnnotationHubData' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'AnnotationHubData:::.httrFileInfo' 'GenomeInfoDb:::.taxonomyId'
  See the note in ?`:::` about the use of this operator.
package 'methods' is used but not declared
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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
  'E:/biocbld/bbs-3.3-bioc/meat/ProteomicsAnnotationHubData.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ProteomicsAnnotationHubData' ...
** 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 'ProteomicsAnnotationHubData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ProteomicsAnnotationHubData' as ProteomicsAnnotationHubData_1.2.2.zip
* DONE (ProteomicsAnnotationHubData)

name	user	system	elapsed
ProteomicsAnnotationHubData	0	0	0
readPahdFiles	0.00	0.01	0.01
writePahdTemplate	0.03	0.00	0.04

name	user	system	elapsed
ProteomicsAnnotationHubData	0	0	0
readPahdFiles	0	0	0
writePahdTemplate	0.01	0.00	0.02