Back to the "Multiple platform build/check report" A  B  C  D  E [F] G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for frmaTools on moscato1

This page was generated on 2016-09-21 03:42:55 -0700 (Wed, 21 Sep 2016).

Package 443/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
frmaTools 1.25.0
Matthew N. McCall
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/frmaTools
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: frmaTools
Version: 1.25.0
Command: rm -rf frmaTools.buildbin-libdir frmaTools.Rcheck && mkdir frmaTools.buildbin-libdir frmaTools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=frmaTools.buildbin-libdir frmaTools_1.25.0.tar.gz >frmaTools.Rcheck\00install.out 2>&1 && cp frmaTools.Rcheck\00install.out frmaTools-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=frmaTools.buildbin-libdir --install="check:frmaTools-install.out" --force-multiarch --no-vignettes --timings frmaTools_1.25.0.tar.gz
StartedAt: 2016-09-20 08:31:05 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:32:11 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 65.9 seconds
RetCode: 0
Status:  OK  
CheckDir: frmaTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf frmaTools.buildbin-libdir frmaTools.Rcheck && mkdir frmaTools.buildbin-libdir frmaTools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=frmaTools.buildbin-libdir frmaTools_1.25.0.tar.gz >frmaTools.Rcheck\00install.out 2>&1 && cp frmaTools.Rcheck\00install.out frmaTools-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=frmaTools.buildbin-libdir --install="check:frmaTools-install.out" --force-multiarch --no-vignettes --timings frmaTools_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/frmaTools.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 'frmaTools/DESCRIPTION' ... OK
* this is package 'frmaTools' version '1.25.0'
* 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 ... NOTE
Found the following hidden files and directories:
  inst/VectorPkg-template/data/.dummy.txt
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'frmaTools' 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 'oligo' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'affy'
  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
convertPlatform: no visible global function definition for
  'cleancdfname'
convertPlatform: no visible global function definition for 'cdfName'
convertPlatform: no visible global function definition for 'probeNames'
convertPlatform: no visible global function definition for 'pmindex'
getFidMetaProbesetCore: no visible global function definition for 'db'
getFidMetaProbesetExtended: no visible global function definition for
  'db'
getFidMetaProbesetFull: no visible global function definition for 'db'
getFidProbeset: no visible global function definition for 'db'
makeMaps: no visible global function definition for 'xy2indices'
makeVectorsAffyBatch: no visible global function definition for
  'ReadAffy'
makeVectorsAffyBatch: no visible global function definition for
  'bg.correct.rma'
makeVectorsAffyBatch: no visible global function definition for 'pm'
makeVectorsAffyBatch: no visible global function definition for
  'probeNames'
makeVectorsAffyBatch: no visible global function definition for
  'pmindex'
makeVectorsAffyBatch: no visible global function definition for
  'packageVersion'
makeVectorsFeatureSet: no visible global function definition for
  'read.celfiles'
makeVectorsFeatureSet: no visible global function definition for
  'backgroundCorrect'
Undefined global functions or variables:
  ReadAffy backgroundCorrect bg.correct.rma cdfName cleancdfname db
  packageVersion pm pmindex probeNames read.celfiles xy2indices
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
* 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
convertPlatform 7.25   0.08    9.04
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
convertPlatform  7.4   0.06    7.46
* 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: 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/frmaTools.Rcheck/00check.log'
for details.


frmaTools.Rcheck/00install.out:


install for i386

* installing *source* package 'frmaTools' ...
** 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 'frmaTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'frmaTools' as frmaTools_1.25.0.zip
* DONE (frmaTools)

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

nameusersystemelapsed
convertPlatform7.250.089.04
makeVectorPackage000

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

nameusersystemelapsed
convertPlatform7.400.067.46
makeVectorPackage000