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BioC 3.2: CHECK report for AnnotationFuncs on moscato1

This page was generated on 2016-04-23 10:17:48 -0700 (Sat, 23 Apr 2016).

Package 46/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationFuncs 1.20.0
Stefan McKinnon Edwards
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/AnnotationFuncs
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationFuncs
Version: 1.20.0
Command: rm -rf AnnotationFuncs.buildbin-libdir AnnotationFuncs.Rcheck && mkdir AnnotationFuncs.buildbin-libdir AnnotationFuncs.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationFuncs.buildbin-libdir AnnotationFuncs_1.20.0.tar.gz >AnnotationFuncs.Rcheck\00install.out 2>&1 && cp AnnotationFuncs.Rcheck\00install.out AnnotationFuncs-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=AnnotationFuncs.buildbin-libdir --install="check:AnnotationFuncs-install.out" --force-multiarch --no-vignettes --timings AnnotationFuncs_1.20.0.tar.gz
StartedAt: 2016-04-22 23:32:15 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:35:17 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 181.7 seconds
RetCode: 0
Status:  OK  
CheckDir: AnnotationFuncs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AnnotationFuncs.buildbin-libdir AnnotationFuncs.Rcheck && mkdir AnnotationFuncs.buildbin-libdir AnnotationFuncs.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationFuncs.buildbin-libdir AnnotationFuncs_1.20.0.tar.gz >AnnotationFuncs.Rcheck\00install.out 2>&1 && cp AnnotationFuncs.Rcheck\00install.out AnnotationFuncs-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=AnnotationFuncs.buildbin-libdir --install="check:AnnotationFuncs-install.out" --force-multiarch --no-vignettes --timings AnnotationFuncs_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/AnnotationFuncs.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationFuncs/DESCRIPTION' ... OK
* this is package 'AnnotationFuncs' version '1.20.0'
* 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 'AnnotationFuncs' 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
Package in Depends field not imported from: 'AnnotationDbi'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getOrthologs: no visible global function definition for 'dbmeta'
getOrthologs: no visible global function definition for 'dbconn'
getOrthologs: no visible global function definition for 'dbListTables'
getOrthologs: no visible global function definition for 'dbConnect'
getOrthologs: no visible global function definition for 'dbDriver'
getOrthologs: no visible global function definition for 'dbSendQuery'
getOrthologs: no visible global function definition for 'dbfile'
getOrthologs: no visible global function definition for 'dbClearResult'
getOrthologs: no visible global function definition for 'dbWriteTable'
getOrthologs: no visible global function definition for 'direction'
getOrthologs: no visible global function definition for 'dbGetQuery'
getOrthologs: no visible global function definition for 'dbDisconnect'
translate: no visible global function definition for 'dbmeta'
translate: no visible global function definition for 'dbconn'
* 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' ... [63s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
AnnotationFuncs-package 0.66   0.02   25.72
getOrthologs            0.64   0.01   25.35
** running examples for arch 'x64' ... [7s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/AnnotationFuncs.Rcheck/00check.log'
for details.


AnnotationFuncs.Rcheck/00install.out:


install for i386

* installing *source* package 'AnnotationFuncs' ...
** 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 'AnnotationFuncs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationFuncs' as AnnotationFuncs_1.20.0.zip
* DONE (AnnotationFuncs)

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

nameusersystemelapsed
AnnotationFuncs-package 0.66 0.0225.72
getEvidenceCodes000
getOrthologs 0.64 0.0125.35
mapLists000
pickGO0.030.004.60
pickRefSeq0.060.001.82
removeNAs000
translate0.240.001.83

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

nameusersystemelapsed
AnnotationFuncs-package0.640.000.64
getEvidenceCodes000
getOrthologs0.590.021.63
mapLists000
pickGO0.060.000.06
pickRefSeq0.210.000.21
removeNAs000
translate0.170.010.18