BioC 3.2: CHECK report for synlet on linux1.bioconductor.org
This page was generated on 2015-10-27 17:27:23 -0400 (Tue, 27 Oct 2015).
synlet 1.0.0 Chunxuan Shao
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/synlet | Last Changed Rev: 109589 / Revision: 109947 | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |  |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |  |
Summary
Package: synlet |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings synlet_1.0.0.tar.gz |
StartedAt: 2015-10-27 08:36:45 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 08:37:48 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 63.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: synlet.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings synlet_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/synlet.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘synlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synlet’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘synlet’ can be installed ... [5s/5s] 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 loading without being on the library search path ... 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
.ff_bscorePlate: no visible binding for global variable ‘PLATE’
.ff_bscorePlate: no visible binding for global variable
‘EXPERIMENT_TYPE’
.ff_contsiRNANorm: no visible binding for global variable
‘MASTER_PLATE’
.ff_contsiRNANorm: no visible binding for global variable
‘EXPERIMENT_TYPE’
.ff_contsiRNANorm: no visible binding for global variable
‘WELL_CONTENT_NAME’
.ff_masterPlateValue: no visible binding for global variable
‘EXPERIMENT_MODIFICATION’
.ff_plateNorm: no visible binding for global variable ‘MASTER_PLATE’
.ff_plateNorm: no visible binding for global variable ‘EXPERIMENT_TYPE’
.ff_plateNorm: no visible binding for global variable
‘WELL_CONTENT_NAME’
bScore: no visible binding for global variable
‘EXPERIMENT_MODIFICATION’
bScore: no visible binding for global variable ‘MASTER_PLATE’
plateHeatmap: no visible binding for global variable ‘COL_NAME’
plateHeatmap: no visible binding for global variable ‘ROW_NAME’
plateHeatmap: no visible binding for global variable ‘value’
scatterPlot: no visible binding for global variable ‘READOUT’
scatterPlot: no visible binding for global variable ‘condition’
siRNAPlot: no visible binding for global variable ‘WELL_CONTENT_NAME’
siRNAPlot: no visible binding for global variable ‘READOUT’
siRNAPlot: no visible binding for global variable ‘PLATE’
siRNAPlot: no visible binding for global variable ‘MASTER_PLATE’
siRNAPlot: no visible binding for global variable ‘Var1’
siRNAPlot: no visible binding for global variable ‘value’
siRNAPlot: no visible binding for global variable ‘siRNA’
siRNAPlot: no visible binding for global variable ‘experiments’
zFactor: no visible binding for global variable ‘condition’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [2s/2s]
[3s/3s] OK
* 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 NOTE
See
‘/home/biocbuild/bbs-3.2-bioc/meat/synlet.Rcheck/00check.log’
for details.
synlet.Rcheck/00install.out:
* installing *source* package ‘synlet’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (synlet)
synlet.Rcheck/synlet-Ex.timings:
name | user | system | elapsed
|
bScore | 0.188 | 0.000 | 0.188 |
|
madSelect | 0.096 | 0.003 | 0.099 |
|
plateHeatmap | 0.758 | 0.004 | 0.764 |
|
rankProdHits | 1.666 | 0.004 | 1.673 |
|
rsaHits | 0.157 | 0.004 | 0.160 |
|
scatterPlot | 0.444 | 0.000 | 0.445 |
|
siRNAPlot | 2.850 | 0.004 | 2.857 |
|
tTest | 1.068 | 0.000 | 1.068 |
|
zFactor | 0.022 | 0.000 | 0.021 |
|