Back to Multiple platform build/check report for BioC 3.9
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for ArrayExpress on tokay2

This page was generated on 2019-04-09 11:56:41 -0400 (Tue, 09 Apr 2019).

Package 72/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.43.0
Suhaib Mohammed
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/ArrayExpress
Branch: master
Last Commit: 09e0a49
Last Changed Date: 2018-10-30 11:54:28 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: ArrayExpress
Version: 1.43.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ArrayExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ArrayExpress_1.43.0.tar.gz
StartedAt: 2019-04-09 01:07:01 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:12:11 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 310.2 seconds
RetCode: 0
Status:  OK  
CheckDir: ArrayExpress.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ArrayExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ArrayExpress_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ArrayExpress.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.43.0'
* 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 '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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ArrayExpress 10.45   1.00   18.67
getAE         3.56   0.53    8.12
queryAE       2.36   0.23   11.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ArrayExpress 10.70   1.11   17.30
getAE         3.34   0.31   18.17
queryAE       2.55   0.03   10.17
* 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-3.9-bioc/meat/ArrayExpress.Rcheck/00check.log'
for details.



Installation output

ArrayExpress.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ArrayExpress_1.43.0.tar.gz && rm -rf ArrayExpress.buildbin-libdir && mkdir ArrayExpress.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ArrayExpress.buildbin-libdir ArrayExpress_1.43.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ArrayExpress_1.43.0.zip && rm ArrayExpress_1.43.0.tar.gz ArrayExpress_1.43.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 41498  100 41498    0     0   630k      0 --:--:-- --:--:-- --:--:--  710k

install for i386

* installing *source* package 'ArrayExpress' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ArrayExpress'
    finding HTML links ... done
    ArrayExpress                            html  
    ae2bioc                                 html  
    extract.zip                             html  
    getAE                                   html  
    getcolproc                              html  
    getcolraw                               html  
    procset                                 html  
    queryAE                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ArrayExpress' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ArrayExpress' as ArrayExpress_1.43.0.zip
* DONE (ArrayExpress)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ArrayExpress' successfully unpacked and MD5 sums checked

Tests output


Example timings

ArrayExpress.Rcheck/examples_i386/ArrayExpress-Ex.timings

nameusersystemelapsed
ArrayExpress10.45 1.0018.67
ae2bioc000
getAE3.560.538.12
procset000
queryAE 2.36 0.2311.08

ArrayExpress.Rcheck/examples_x64/ArrayExpress-Ex.timings

nameusersystemelapsed
ArrayExpress10.70 1.1117.30
ae2bioc000
getAE 3.34 0.3118.17
procset000
queryAE 2.55 0.0310.17