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This page was generated on 2022-01-19 13:06:12 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ArrayExpress on tokay2


To the developers/maintainers of the ArrayExpress package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ArrayExpress.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 78/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.54.0  (landing page)
Suhaib Mohammed
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/ArrayExpress
git_branch: RELEASE_3_14
git_last_commit: 9a09ffb
git_last_commit_date: 2021-10-26 11:52:59 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ArrayExpress
Version: 1.54.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ArrayExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ArrayExpress_1.54.0.tar.gz
StartedAt: 2022-01-18 15:33:10 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 15:38:24 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 313.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ArrayExpress.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ArrayExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ArrayExpress_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ArrayExpress.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.54.0'
* 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 (user + system) or elapsed time > 5s
              user system elapsed
ArrayExpress 10.39   1.19   28.75
queryAE       3.82   0.53    9.72
getAE         3.53   0.47   12.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
ArrayExpress 8.70   0.75   30.46
queryAE      4.24   0.11    8.78
getAE        3.50   0.31   11.25
* 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-3.14-bioc/meat/ArrayExpress.Rcheck/00check.log'
for details.



Installation output

ArrayExpress.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ArrayExpress_1.54.0.tar.gz && rm -rf ArrayExpress.buildbin-libdir && mkdir ArrayExpress.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ArrayExpress.buildbin-libdir ArrayExpress_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ArrayExpress_1.54.0.zip && rm ArrayExpress_1.54.0.tar.gz ArrayExpress_1.54.0.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 41397  100 41397    0     0   377k      0 --:--:-- --:--:-- --:--:--  381k

install for i386

* installing *source* package 'ArrayExpress' ...
** using staged installation
** 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_1.54.0.zip
* DONE (ArrayExpress)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ArrayExpress' successfully unpacked and MD5 sums checked

Tests output


Example timings

ArrayExpress.Rcheck/examples_i386/ArrayExpress-Ex.timings

nameusersystemelapsed
ArrayExpress10.39 1.1928.75
ae2bioc000
getAE 3.53 0.4712.05
procset000
queryAE3.820.539.72

ArrayExpress.Rcheck/examples_x64/ArrayExpress-Ex.timings

nameusersystemelapsed
ArrayExpress 8.70 0.7530.46
ae2bioc000
getAE 3.50 0.3111.25
procset000
queryAE4.240.118.78