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BioC 3.5: CHECK report for synlet on veracruz2

This page was generated on 2017-10-18 14:33:32 -0400 (Wed, 18 Oct 2017).

Package 1301/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
synlet 1.6.0
Chunxuan Shao
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/synlet
Branch: RELEASE_3_5
Last Commit: c379737
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: synlet
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings synlet_1.6.0.tar.gz
StartedAt: 2017-10-18 09:35:39 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 09:37:11 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 92.2 seconds
RetCode: 0
Status:  OK 
CheckDir: synlet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings synlet_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/synlet.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 ‘synlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synlet’ version ‘1.6.0’
* 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 ... 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_bscorePlate: no visible global function definition for ‘medpolish’
.ff_bscorePlate: no visible global function definition for ‘mad’
.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_contsiRNANorm: no visible binding for global variable ‘median’
.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’
.ff_plateNorm: no visible binding for global variable ‘median’
.ff_ratio_madS: no visible global function definition for ‘median’
.ff_ratio_rsa: no visible global function definition for ‘median’
.ff_ttest: no visible global function definition for ‘t.test’
.ff_ttest: no visible global function definition for ‘is’
OPIScore: no visible global function definition for ‘phyper’
bScore: no visible binding for global variable
  ‘EXPERIMENT_MODIFICATION’
bScore: no visible binding for global variable ‘MASTER_PLATE’
bScore: no visible global function definition for ‘write.table’
madSelect: no visible global function definition for ‘write.table’
madSelect: no visible global function definition for ‘median’
madSelect: no visible global function definition for ‘mad’
plateHeatmap: no visible global function definition for
  ‘colorRampPalette’
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’
rsaHits: no visible global function definition for ‘write.table’
scatterPlot: no visible binding for global variable ‘READOUT’
scatterPlot: no visible binding for global variable ‘condition’
siRNAPlot: no visible global function definition for ‘rainbow’
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’
siRNAPlot: no visible global function definition for ‘pdf’
siRNAPlot: no visible global function definition for ‘dev.off’
tTest: no visible global function definition for ‘p.adjust’
zFactor: no visible binding for global variable ‘condition’
zFactor: no visible binding for global variable ‘sd’
zFactor: no visible binding for global variable ‘median’
zFactor: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  COL_NAME EXPERIMENT_MODIFICATION EXPERIMENT_TYPE MASTER_PLATE PLATE
  READOUT ROW_NAME Var1 WELL_CONTENT_NAME colorRampPalette
  complete.cases condition dev.off experiments is mad median medpolish
  p.adjust pdf phyper rainbow sd siRNA t.test value write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("methods", "is")
  importFrom("stats", "complete.cases", "mad", "median", "medpolish",
             "p.adjust", "phyper", "sd", "t.test")
  importFrom("utils", "write.table")
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 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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
  ‘/Users/biocbuild/bbs-3.5-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:

nameusersystemelapsed
bScore0.7060.0100.735
madSelect0.4470.0040.460
plateHeatmap3.0240.0373.162
rankProdHits1.3340.0321.415
rsaHits0.2440.0020.257
scatterPlot0.8980.0080.931
siRNAPlot4.2050.0254.406
tTest1.4640.0091.515
zFactor0.0280.0010.029