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BioC 3.5: CHECK report for miRNApath on tokay2

This page was generated on 2017-08-16 13:19:59 -0400 (Wed, 16 Aug 2017).

Package 830/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRNApath 1.36.0
James M. Ward
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/miRNApath
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: miRNApath
Version: 1.36.0
Command: rm -rf miRNApath.buildbin-libdir miRNApath.Rcheck && mkdir miRNApath.buildbin-libdir miRNApath.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=miRNApath.buildbin-libdir miRNApath_1.36.0.tar.gz >miRNApath.Rcheck\00install.out 2>&1 && cp miRNApath.Rcheck\00install.out miRNApath-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=miRNApath.buildbin-libdir --install="check:miRNApath-install.out" --force-multiarch --no-vignettes --timings miRNApath_1.36.0.tar.gz
StartedAt: 2017-08-16 01:19:21 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:20:12 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 51.0 seconds
RetCode: 0
Status:  OK  
CheckDir: miRNApath.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf miRNApath.buildbin-libdir miRNApath.Rcheck && mkdir miRNApath.buildbin-libdir miRNApath.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=miRNApath.buildbin-libdir miRNApath_1.36.0.tar.gz >miRNApath.Rcheck\00install.out 2>&1 && cp miRNApath.Rcheck\00install.out miRNApath-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=miRNApath.buildbin-libdir --install="check:miRNApath-install.out" --force-multiarch --no-vignettes --timings miRNApath_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/miRNApath.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'miRNApath/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'miRNApath' version '1.36.0'
* 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 'miRNApath' 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 ... NOTE
Warning: no function found corresponding to methods exports from 'miRNApath' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: no function found corresponding to methods exports from 'miRNApath' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'methods'
  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
loadmirnapath: no visible global function definition for 'read.table'
loadmirnapath: no visible global function definition for 'new'
loadmirnapathways: no visible global function definition for
  'read.table'
loadmirnatogene: no visible global function definition for 'read.table'
mirnaTable: no visible global function definition for 'reshape'
runEnrichment : <anonymous> : <anonymous>: no visible global function
  definition for 'phyper'
runEnrichment: no visible global function definition for 'slotNames'
Undefined global functions or variables:
  new phyper read.table reshape slotNames
Consider adding
  importFrom("methods", "new", "slotNames")
  importFrom("stats", "phyper", "reshape")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
mirnaTable 6.32   0.01    6.35
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
mirnaTable 8.04   0.02    8.05
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/miRNApath.Rcheck/00check.log'
for details.


miRNApath.Rcheck/00install.out:


install for i386

* installing *source* package 'miRNApath' ...
** 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 'miRNApath' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'miRNApath' as miRNApath_1.36.0.zip
* DONE (miRNApath)

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

nameusersystemelapsed
checkColumns000
convertFoldChange000
filtermirnapath0.100.000.09
loadmirnapath0.090.020.13
loadmirnapathways0.140.000.14
loadmirnatogene0.160.030.19
miRNApath-package0.020.000.01
mirnaTable6.320.016.35
mirnaobj0.030.000.03
mirnapath-class0.020.000.01
runEnrichment000

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

nameusersystemelapsed
checkColumns000
convertFoldChange000
filtermirnapath0.080.000.07
loadmirnapath0.110.010.13
loadmirnapathways0.140.000.14
loadmirnatogene0.170.020.19
miRNApath-package000
mirnaTable8.040.028.05
mirnaobj0.010.000.02
mirnapath-class0.030.000.03
runEnrichment000