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BioC 3.1: CHECK report for ensembldb on moscato2

This page was generated on 2015-10-09 09:32:11 -0700 (Fri, 09 Oct 2015).

Package 300/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ensembldb 1.0.1
Johannes Rainer
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ensembldb
Last Changed Rev: 104822 / Revision: 109384
Last Changed Date: 2015-06-11 00:11:17 -0700 (Thu, 11 Jun 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ensembldb
Version: 1.0.1
Command: rm -rf ensembldb.buildbin-libdir ensembldb.Rcheck && mkdir ensembldb.buildbin-libdir ensembldb.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ensembldb.buildbin-libdir ensembldb_1.0.1.tar.gz >ensembldb.Rcheck\00install.out 2>&1 && cp ensembldb.Rcheck\00install.out ensembldb-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ensembldb.buildbin-libdir --install="check:ensembldb-install.out" --force-multiarch --no-vignettes --timings ensembldb_1.0.1.tar.gz
StartedAt: 2015-10-09 01:29:34 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:35:34 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 359.8 seconds
RetCode: 0
Status:  OK  
CheckDir: ensembldb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ensembldb.buildbin-libdir ensembldb.Rcheck && mkdir ensembldb.buildbin-libdir ensembldb.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ensembldb.buildbin-libdir ensembldb_1.0.1.tar.gz >ensembldb.Rcheck\00install.out 2>&1 && cp ensembldb.Rcheck\00install.out ensembldb-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ensembldb.buildbin-libdir --install="check:ensembldb-install.out" --force-multiarch --no-vignettes --timings ensembldb_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/ensembldb.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 'ensembldb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ensembldb' 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 'ensembldb' 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
Unexported objects imported by ':::' calls:
  'GenomicFeatures:::fetchChromLengthsFromEnsembl'
  'GenomicFeatures:::fetchChromLengthsFromEnsemblPlants'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
exons,EnsDb : .local: no visible binding for global variable 'group.by'
exons,EnsDb : .local: no visible global function definition for
  'IRanges'
exonsBy,EnsDb : .local: no visible global function definition for
  'IRanges'
genes,EnsDb : .local: no visible global function definition for
  'IRanges'
transcripts,EnsDb : .local: no visible binding for global variable
  'group.by'
transcripts,EnsDb : .local: no visible global function definition for
  'IRanges'
transcriptsBy,EnsDb : .local: no visible global function definition for
  'IRanges'
* 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' ... [58s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
EnsDb-exonsBy 6.66   0.93   12.57
EnsDb-class   4.61   0.99   36.99
** running examples for arch 'x64' ... [23s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
EnsDb-exonsBy 5.98   0.88    7.08
EnsDb-class   4.61   0.57    5.20
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [24s]
 [24s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [30s]
 [31s] 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: 2 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/ensembldb.Rcheck/00check.log'
for details.


ensembldb.Rcheck/00install.out:


install for i386

* installing *source* package 'ensembldb' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'ensembldb' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'ensembldb' as ensembldb_1.0.1.zip
* DONE (ensembldb)

ensembldb.Rcheck/examples_i386/ensembldb-Ex.timings:

nameusersystemelapsed
EnsDb-class 4.61 0.9936.99
EnsDb-exonsBy 6.66 0.9312.57
GeneidFilter-class000
SeqendFilter0.020.000.01
makeEnsemblDbPackage0.550.000.55

ensembldb.Rcheck/examples_x64/ensembldb-Ex.timings:

nameusersystemelapsed
EnsDb-class4.610.575.20
EnsDb-exonsBy5.980.887.08
GeneidFilter-class0.020.000.02
SeqendFilter0.010.000.01
makeEnsemblDbPackage0.660.040.75