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BioC 3.4: CHECK report for PROMISE on tokay1

This page was generated on 2017-04-15 16:16:14 -0400 (Sat, 15 Apr 2017).

Package 955/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PROMISE 1.26.0
Stan Pounds , Xueyuan Cao
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/PROMISE
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / 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: PROMISE
Version: 1.26.0
Command: rm -rf PROMISE.buildbin-libdir PROMISE.Rcheck && mkdir PROMISE.buildbin-libdir PROMISE.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PROMISE.buildbin-libdir PROMISE_1.26.0.tar.gz >PROMISE.Rcheck\00install.out 2>&1 && cp PROMISE.Rcheck\00install.out PROMISE-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=PROMISE.buildbin-libdir --install="check:PROMISE-install.out" --force-multiarch --no-vignettes --timings PROMISE_1.26.0.tar.gz
StartedAt: 2017-04-15 00:11:49 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:13:44 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 114.7 seconds
RetCode: 0
Status:  OK  
CheckDir: PROMISE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PROMISE.buildbin-libdir PROMISE.Rcheck && mkdir PROMISE.buildbin-libdir PROMISE.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PROMISE.buildbin-libdir PROMISE_1.26.0.tar.gz >PROMISE.Rcheck\00install.out 2>&1 && cp PROMISE.Rcheck\00install.out PROMISE-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=PROMISE.buildbin-libdir --install="check:PROMISE-install.out" --force-multiarch --no-vignettes --timings PROMISE_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/PROMISE.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PROMISE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PROMISE' version '1.26.0'
* 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 'PROMISE' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase' 'GSEABase'
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
jung.rstat: no visible binding for global variable 'var'
jung.rstat: no visible global function definition for 'var'
spearman.rstat: no visible global function definition for 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
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 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
** running examples for arch 'x64' ... 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:/Users/biocbuild/bbs-3.4-bioc/meat/PROMISE.Rcheck/00check.log'
for details.


PROMISE.Rcheck/00install.out:


install for i386

* installing *source* package 'PROMISE' ...
** 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 'PROMISE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PROMISE' as PROMISE_1.26.0.zip
* DONE (PROMISE)

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

nameusersystemelapsed
PROMISE-package2.490.022.50
PROMISE2.480.002.49
avg.abs.genestat0.020.000.01
jung.rstat0.000.010.02
promise.genestat0.030.020.04
spearman.rstat0.010.000.02

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

nameusersystemelapsed
PROMISE-package2.600.032.64
PROMISE2.650.012.66
avg.abs.genestat0.020.000.02
jung.rstat000
promise.genestat0.040.020.06
spearman.rstat0.000.020.02