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 | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### 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
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* 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.
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)