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BioC 3.2: CHECK report for annaffy on windows1.bioconductor.org

This page was generated on 2015-10-27 17:27:38 -0400 (Tue, 27 Oct 2015).

Package 41/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annaffy 1.42.0
Colin A. Smith
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/annaffy
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: annaffy
Version: 1.42.0
Command: rm -rf annaffy.buildbin-libdir annaffy.Rcheck && mkdir annaffy.buildbin-libdir annaffy.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annaffy.buildbin-libdir annaffy_1.42.0.tar.gz >annaffy.Rcheck\00install.out 2>&1 && cp annaffy.Rcheck\00install.out annaffy-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=annaffy.buildbin-libdir --install="check:annaffy-install.out" --force-multiarch --no-vignettes --timings annaffy_1.42.0.tar.gz
StartedAt: 2015-10-26 23:42:59 -0400 (Mon, 26 Oct 2015)
EndedAt: 2015-10-26 23:44:42 -0400 (Mon, 26 Oct 2015)
EllapsedTime: 102.9 seconds
RetCode: 0
Status:  OK  
CheckDir: annaffy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf annaffy.buildbin-libdir annaffy.Rcheck && mkdir annaffy.buildbin-libdir annaffy.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annaffy.buildbin-libdir annaffy_1.42.0.tar.gz >annaffy.Rcheck\00install.out 2>&1 && cp annaffy.Rcheck\00install.out annaffy-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=annaffy.buildbin-libdir --install="check:annaffy-install.out" --force-multiarch --no-vignettes --timings annaffy_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/annaffy.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annaffy/DESCRIPTION' ... OK
* this is package 'annaffy' version '1.42.0'
* 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 'annaffy' 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
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'tcltk' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'GO.db' 'KEGG.db' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing object imported by a ':::' call: 'Biobase:::biocReposList'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'annaffy/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

.aaf.goterm: no visible binding for global variable 'GOTERM'
aafGO: no visible global function definition for 'dbGetQuery'
aafGO: no visible global function definition for 'GO_dbfile'
aafPathway: no visible binding for global variable 'KEGGPATHID2NAME'
aafTableInt: no visible global function definition for 'sampleNames'
aafTableInt: no visible global function definition for 'featureNames'
aafTableInt: no visible global function definition for 'exprs'
chkPkgs: no visible global function definition for 'userQuery'
selectorWidget : move: no visible global function definition for
  'tkcurselection'
selectorWidget : move: no visible global function definition for
  'tclvalue'
selectorWidget : move: no visible global function definition for
  'tkget'
selectorWidget : move: no visible global function definition for
  'tkinsert'
selectorWidget : move: no visible global function definition for
  'tkdelete'
selectorWidget : move: no visible global function definition for
  'tkselection.clear'
selectorWidget : ok: no visible global function definition for 'tkget'
selectorWidget : ok: no visible global function definition for
  'tkdestroy'
selectorWidget: no visible global function definition for 'tktoplevel'
selectorWidget: no visible global function definition for 'tkwm.title'
selectorWidget: no visible global function definition for
  'tkwm.resizable'
selectorWidget: no visible global function definition for 'tkframe'
selectorWidget: no visible global function definition for 'tklistbox'
selectorWidget : <anonymous>: no visible global function definition for
  'tkset'
selectorWidget: no visible global function definition for 'tkscrollbar'
selectorWidget : <anonymous>: no visible global function definition for
  'tkyview'
selectorWidget: no visible global function definition for 'tkgrid'
selectorWidget: no visible global function definition for 'tklabel'
selectorWidget: no visible global function definition for 'tkbutton'
selectorWidget: no visible global function definition for 'tkinsert'
selectorWidget : <anonymous>: no visible global function definition for
  'tkdestroy'
selectorWidget: no visible global function definition for 'tkbind'
selectorWidget: no visible global function definition for
  'tkwait.window'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [10s] OK
** 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
  'C:/biocbld/bbs-3.2-bioc/meat/annaffy.Rcheck/00check.log'
for details.


annaffy.Rcheck/00install.out:


install for i386

* installing *source* package 'annaffy' ...
** R
** data
** 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 'annaffy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'annaffy' as annaffy_1.42.0.zip
* DONE (annaffy)

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

nameusersystemelapsed
aafChromLoc0.330.030.44
aafChromosome0.060.030.14
aafCytoband0.050.010.13
aafDescription0.080.000.08
aafGO0.410.082.69
aafGenBank0.040.000.09
aafLocusLink0.050.000.05
aafPathway0.350.000.36
aafProbe0.040.000.05
aafPubMed0.160.031.26
aafSearchText0.640.030.67
aafSymbol0.040.000.03
aafUniGene0.030.000.17
is.annpkg0.760.321.17

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

nameusersystemelapsed
aafChromLoc0.360.010.37
aafChromosome0.060.000.07
aafCytoband0.050.000.04
aafDescription0.040.020.07
aafGO0.490.010.50
aafGenBank0.080.000.07
aafLocusLink0.060.000.07
aafPathway0.440.020.45
aafProbe0.040.000.05
aafPubMed0.180.000.17
aafSearchText0.750.000.75
aafSymbol0.180.000.19
aafUniGene0.050.000.04
is.annpkg0.600.260.94