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BioC 3.4: CHECK report for OrganismDbi on moscato1

This page was generated on 2016-09-21 03:44:21 -0700 (Wed, 21 Sep 2016).

Package 852/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OrganismDbi 1.15.1
Biocore Data Team
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OrganismDbi
Last Changed Rev: 117534 / Revision: 121152
Last Changed Date: 2016-05-16 07:31:22 -0700 (Mon, 16 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: OrganismDbi
Version: 1.15.1
Command: rm -rf OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && mkdir OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrganismDbi.buildbin-libdir OrganismDbi_1.15.1.tar.gz >OrganismDbi.Rcheck\00install.out 2>&1 && cp OrganismDbi.Rcheck\00install.out OrganismDbi-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=OrganismDbi.buildbin-libdir --install="check:OrganismDbi-install.out" --force-multiarch --no-vignettes --timings OrganismDbi_1.15.1.tar.gz
StartedAt: 2016-09-20 13:27:24 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:50:13 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 1369.3 seconds
RetCode: 0
Status:  OK  
CheckDir: OrganismDbi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && mkdir OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrganismDbi.buildbin-libdir OrganismDbi_1.15.1.tar.gz >OrganismDbi.Rcheck\00install.out 2>&1 && cp OrganismDbi.Rcheck\00install.out OrganismDbi-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=OrganismDbi.buildbin-libdir --install="check:OrganismDbi-install.out" --force-multiarch --no-vignettes --timings OrganismDbi_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/OrganismDbi.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 'OrganismDbi/DESCRIPTION' ... OK
* this is package 'OrganismDbi' version '1.15.1'
* 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 'OrganismDbi' 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 object imported by a ':::' call: 'BiocGenerics:::testPackage'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.biocAnnPackages' '.extractPkgsAndCols' '.gentlyExtractDbFiles'
  '.lookupDbNameFromKeytype' '.mungeGraphData' '.taxIdToOrgDb'
  '.taxIdToOrgDbName' '.testGraphData' '.testKeys' 'OrganismDb'
* 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
Examples with CPU or elapsed time > 5s
                           user system elapsed
makeOrganismDbFromBiomart 17.23   0.74   55.68
rangeBasedAccessors        8.69   0.08    8.77
OrganismDb                 7.67   0.08    8.55
makeOrganismDbFromTxDb     6.52   0.07   78.74
makeOrganismDbFromUCSC     5.79   0.14   80.10
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
makeOrganismDbFromBiomart 13.76   0.56   41.24
rangeBasedAccessors       10.50   0.04   10.55
OrganismDb                 8.75   0.08   10.11
makeOrganismDbFromUCSC     5.87   0.13   73.43
makeOrganismDbFromTxDb     5.68   0.09   72.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'OrganismDbi_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'OrganismDbi_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/OrganismDbi.Rcheck/00check.log'
for details.


OrganismDbi.Rcheck/00install.out:


install for i386

* installing *source* package 'OrganismDbi' ...
** 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 'OrganismDbi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OrganismDbi' as OrganismDbi_1.15.1.zip
* DONE (OrganismDbi)

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

nameusersystemelapsed
OrganismDb7.670.088.55
coordinate-mapping-method1.040.011.06
makeOrganismDbFromBiomart17.23 0.7455.68
makeOrganismDbFromTxDb 6.52 0.0778.74
makeOrganismDbFromUCSC 5.79 0.1480.10
makeOrganismPackage000
rangeBasedAccessors8.690.088.77

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

nameusersystemelapsed
OrganismDb 8.75 0.0810.11
coordinate-mapping-method1.080.031.11
makeOrganismDbFromBiomart13.76 0.5641.24
makeOrganismDbFromTxDb 5.68 0.0972.39
makeOrganismDbFromUCSC 5.87 0.1373.43
makeOrganismPackage000
rangeBasedAccessors10.50 0.0410.55