Suhaib Mohammed
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/ArrayExpress |
| Branch: RELEASE_3_10 |
| Last Commit: 4eb2ee5 |
| Last Changed Date: 2019-10-29 13:07:58 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:18:36 -0400 (Wed, 15 Apr 2020).
| Package 77/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ArrayExpress 1.46.0 Suhaib Mohammed
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ArrayExpress |
| Version: 1.46.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ArrayExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ArrayExpress_1.46.0.tar.gz |
| StartedAt: 2020-04-15 01:18:05 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:23:50 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 344.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ArrayExpress.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ArrayExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ArrayExpress_1.46.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ArrayExpress.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.46.0'
* 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
queryAE 9.99 1.05 26.42
ArrayExpress 9.59 0.86 29.92
getAE 3.51 0.33 15.70
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
queryAE 11.87 0.18 26.54
ArrayExpress 7.12 0.90 21.12
getAE 3.50 0.25 12.08
* 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-3.10-bioc/meat/ArrayExpress.Rcheck/00check.log'
for details.
ArrayExpress.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/ArrayExpress_1.46.0.tar.gz && rm -rf ArrayExpress.buildbin-libdir && mkdir ArrayExpress.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ArrayExpress.buildbin-libdir ArrayExpress_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ArrayExpress_1.46.0.zip && rm ArrayExpress_1.46.0.tar.gz ArrayExpress_1.46.0.zip
###
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% 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 41615 100 41615 0 0 1112k 0 --:--:-- --:--:-- --:--:-- 1231k
install for i386
* installing *source* package 'ArrayExpress' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
** 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
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
** testing if installed package can be loaded from final location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
** 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
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
* MD5 sums
packaged installation of 'ArrayExpress' as ArrayExpress_1.46.0.zip
* DONE (ArrayExpress)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ArrayExpress' successfully unpacked and MD5 sums checked
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ArrayExpress.Rcheck/examples_i386/ArrayExpress-Ex.timings
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ArrayExpress.Rcheck/examples_x64/ArrayExpress-Ex.timings
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