imageHTS 1.26.0
Joseph Barry
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/imageHTS | | Branch: RELEASE_3_5 | | Last Commit: facaee4 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 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 | [ ERROR ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings imageHTS_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/imageHTS.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘imageHTS/DESCRIPTION’ ... OK
* this is package ‘imageHTS’ version ‘1.26.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘imageHTS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘imageHTS-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fileHTS
> ### Title: Get access to screen data files
> ### Aliases: fileHTS readHTS
>
> ### ** Examples
>
> ## initialize imageHTS object using the local submorph screen
> local = tempdir()
> server = system.file('submorph', package='imageHTS')
> x = parseImageConf('conf/imageconf.txt', localPath=local, serverURL=server)
File "conf/imageconf.txt" read.
Number of plates= 1
Number of replicates= 2
Number of wells= 384
Number of channels= 3
Number of spots= 1
>
> ## fileHTS and readHTS examples
> fileHTS(x, 'file', filename='conf/imageconf.txt')
[1] "/private/tmp/RtmppfCBB0/conf/imageconf.txt"
> fileHTS(x, 'source', uname='001-01-C05', channel=1)
Warning in fileHTS(x, "source", uname = "001-01-C05", channel = 1) :
cannot download the file pointed by "file:///Users/biocbuild/bbs-3.5-bioc/meat/imageHTS.Rcheck/imageHTS/submorph/source/PK-10B-pl1/Well-C005/Tritc.jpeg" to the location "/private/tmp/RtmppfCBB0/source/PK-10B-pl1/Well-C005/Tritc.jpeg"
[1] "/private/tmp/RtmppfCBB0/source/PK-10B-pl1/Well-C005/Tritc.jpeg"
> readHTS(x, 'file', filename='conf/featurepar.txt', format='dcf')
$extractfeatures.method
[1] "getCellFtrsATH"
$cell.classes
[1] "D" "I" "M"
$remove.classification.features
[1] "c.a.m.cx" "c.a.m.cy" "c.t.m.cx" "c.t.m.cy" "c.h.m.cx" "c.h.m.cy"
[7] "c.m.m.cx" "c.m.m.cy" "n.a.m.cx" "n.a.m.cy" "n.t.m.cx" "n.t.m.cy"
[13] "n.h.m.cx" "n.h.m.cy"
$cellHTS.features
[1] "n" "med.c.s.area" "med.c.m.m.eccentricity"
[4] "med.n.ah.cor" "M"
$cellHTS.features.name
[1] "Number of cells" "Median cell size" "Median cell ecc."
[4] "Median A/H nuc. corr." "Metaphase fraction"
>
> ## initialize imageHTS object using the remote kimorph screen
> local = tempdir()
> server = 'http://www.ebi.ac.uk/huber-srv/cellmorph/kimorph/'
> x = parseImageConf('conf/imageconf.txt', localPath=local, serverURL=server)
File "conf/imageconf.txt" read.
Number of plates= 1
Number of replicates= 2
Number of wells= 384
Number of channels= 3
Number of spots= 1
>
> ## get cell features for well '002-02-D06'
> f = readHTS(x, 'ftrs', uname='002-02-D06')
trying URL 'http://www.ebi.ac.uk/huber-srv/cellmorph/kimorph//data/002-02/002-02-D06_ftrs.tab'
Warning in fileHTS(x, type = type, ..., access = access) :
cannot download the file pointed by "http://www.ebi.ac.uk/huber-srv/cellmorph/kimorph//data/002-02/002-02-D06_ftrs.tab" to the location "/private/tmp/RtmppfCBB0/data/002-02/002-02-D06_ftrs.tab"
Error in readHTS(x, "ftrs", uname = "002-02-D06") :
cannot find filename=/private/tmp/RtmppfCBB0/data/002-02/002-02-D06_ftrs.tab
Execution halted
* 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: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/imageHTS.Rcheck/00check.log’
for details.