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BioC 3.5: CHECK report for ArrayExpress on tokay2

This page was generated on 2017-10-18 14:20:13 -0400 (Wed, 18 Oct 2017).

Package 60/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.36.1
Ugis Sarkans
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/ArrayExpress
Branch: RELEASE_3_5
Last Commit: 6cd4c47
Last Changed Date: 2017-10-09 11:28:23 -0400 (Mon, 09 Oct 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: ArrayExpress
Version: 1.36.1
Command: rm -rf ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && mkdir ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayExpress.buildbin-libdir ArrayExpress_1.36.1.tar.gz >ArrayExpress.Rcheck\00install.out 2>&1 && cp ArrayExpress.Rcheck\00install.out ArrayExpress-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ArrayExpress.buildbin-libdir --install="check:ArrayExpress-install.out" --force-multiarch --no-vignettes --timings ArrayExpress_1.36.1.tar.gz
StartedAt: 2017-10-17 22:03:06 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:09:04 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 358.0 seconds
RetCode: 0
Status:  OK  
CheckDir: ArrayExpress.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && mkdir ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayExpress.buildbin-libdir ArrayExpress_1.36.1.tar.gz >ArrayExpress.Rcheck\00install.out 2>&1 && cp ArrayExpress.Rcheck\00install.out ArrayExpress-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ArrayExpress.buildbin-libdir --install="check:ArrayExpress-install.out" --force-multiarch --no-vignettes --timings ArrayExpress_1.36.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ArrayExpress.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ArrayExpress/DESCRIPTION' ... OK
* this is package 'ArrayExpress' version '1.36.1'
* 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 'ArrayExpress' 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.
* 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
ae2bioc: no visible global function definition for 'new'
extract.zip : <anonymous>: no visible global function definition for
  'unzip'
getAE : <anonymous>: no visible global function definition for
  'download.file'
getAE: no visible global function definition for 'download.file'
getDataColsForAE1: no visible global function definition for
  'read.table'
preparePhenoDataFor2channel: no visible global function definition for
  'new'
queryAE: no visible global function definition for 'download.file'
readDerivedDataFiles: no visible global function definition for
  'read.table'
readDerivedDataFiles: no visible global function definition for 'new'
readDerivedDataMatrixFile: no visible global function definition for
  'read.table'
readDerivedDataMatrixFile: no visible global function definition for
  'new'
readExperimentData: no visible global function definition for 'new'
readFeatures: no visible global function definition for 'read.table'
readFeatures: no visible global function definition for 'new'
readPhenoData: no visible global function definition for 'new'
Undefined global functions or variables:
  download.file new read.table unzip
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "download.file", "read.table", "unzip")
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 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
ArrayExpress 9.91   0.95   19.36
getAE        7.05   0.84   36.91
queryAE      2.78   0.06   35.70
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
ArrayExpress 9.87   1.05   14.87
getAE        4.72   0.34    9.54
queryAE      3.54   0.05   10.24
* 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-3.5-bioc/meat/ArrayExpress.Rcheck/00check.log'
for details.


ArrayExpress.Rcheck/00install.out:


install for i386

* installing *source* package 'ArrayExpress' ...
** R
** inst
** preparing package for lazy loading
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'

install for x64

* installing *source* package 'ArrayExpress' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
* MD5 sums
packaged installation of 'ArrayExpress' as ArrayExpress_1.36.1.zip
* DONE (ArrayExpress)

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

nameusersystemelapsed
ArrayExpress 9.91 0.9519.36
ae2bioc000
getAE 7.05 0.8436.91
procset000
queryAE 2.78 0.0635.70

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

nameusersystemelapsed
ArrayExpress 9.87 1.0514.87
ae2bioc000
getAE4.720.349.54
procset000
queryAE 3.54 0.0510.24