erccdashboard 1.7.1
Sarah Munro
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/erccdashboard | | Last Changed Rev: 119665 / Revision: 121152 | | Last Changed Date: 2016-07-26 13:56:03 -0700 (Tue, 26 Jul 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | ERROR | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | ERROR | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | 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 erccdashboard_1.7.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘erccdashboard/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘erccdashboard’ version ‘1.7.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘erccdashboard’ can be installed ... WARNING
Found the following significant warnings:
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/maSignal.Rd:28: unexpected '}'
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/maSignal.Rd:1: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/maSignal.Rd:3: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/maSignal.Rd:5: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/maSignal.Rd:27: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/saveERCCPlots.Rd:104: unexpected '}'
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/saveERCCPlots.Rd:1: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/saveERCCPlots.Rd:3: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/saveERCCPlots.Rd:5: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/saveERCCPlots.Rd:103: All text must be in a section
See ‘/Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00install.out’ for details.
* 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
dynRangePlot: no visible binding for global variable ‘sd’
dynRangePlot: no visible global function definition for ‘loess’
dynRangePlot: no visible global function definition for ‘predict’
dynRangePlot: no visible binding for global variable ‘value’
dynRangePlot: no visible binding for global variable ‘Rep’
dynRangePlot: no visible global function definition for ‘lm’
dynRangePlot: no visible global function definition for ‘coef’
dynRangePlot: no visible global function definition for ‘fivenum’
dynRangePlot: no visible global function definition for ‘IQR’
erccROC: no visible global function definition for ‘read.csv’
estLODR: no visible global function definition for ‘read.csv’
estLODR : LODR: no visible global function definition for ‘preplot’
estLODR : LODR : find.mn: no visible global function definition for
‘preplot’
estLODR : LODR : find.mn: no visible global function definition for
‘qnorm’
estLODR : LODR : segmented.search: no visible global function
definition for ‘preplot’
estLODR : LODR : segmented.search: no visible global function
definition for ‘qnorm’
estLODR : LODR : segmented.search: no visible global function
definition for ‘optimize’
estLODR : LODR: no visible global function definition for ‘residuals’
estLODR : LODR: no visible global function definition for ‘quantile’
estLODR: no visible global function definition for ‘preplot’
estLODR: no visible global function definition for ‘qnorm’
estLODR: no visible global function definition for ‘dev.off’
est_r_m: no visible global function definition for ‘qt’
geneExprTest: no visible global function definition for ‘read.csv’
loadERCCInfo: no visible global function definition for ‘data’
loadERCCInfo: no visible binding for global variable ‘ERCC’
loadERCCInfo: no visible global function definition for ‘read.csv’
maSignal : maStats: no visible global function definition for ‘sd’
maSignal: no visible global function definition for ‘sd’
normalizeDat: no visible binding for global variable ‘quantile’
runDashboard: no visible global function definition for ‘dev.off’
saveERCCPlots: no visible global function definition for ‘png’
saveERCCPlots: no visible global function definition for ‘jpeg’
saveERCCPlots: no visible global function definition for ‘pdf’
saveERCCPlots: no visible global function definition for ‘dev.off’
testDEArray: no visible global function definition for ‘write.csv’
testDECount: no visible global function definition for ‘model.matrix’
testDECount : simcnt.lodr: no visible global function definition for
‘rnbinom’
testDECount: no visible global function definition for ‘write.csv’
testDECount : shrink.phi: no visible global function definition for
‘var’
testDECount : shrink.phi : inverse.trigamma: no visible global function
definition for ‘optimize’
testDECount: no visible global function definition for ‘smooth.spline’
testDECount: no visible global function definition for ‘predict’
Undefined global functions or variables:
ERCC IQR Rep coef data dev.off fivenum jpeg lm loess model.matrix
optimize pdf png predict preplot qnorm qt quantile read.csv residuals
rnbinom sd smooth.spline value var write.csv
Consider adding
importFrom("grDevices", "dev.off", "jpeg", "pdf", "png")
importFrom("stats", "IQR", "coef", "fivenum", "lm", "loess",
"model.matrix", "optimize", "predict", "preplot", "qnorm",
"qt", "quantile", "residuals", "rnbinom", "sd",
"smooth.spline", "var")
importFrom("utils", "data", "read.csv", "write.csv")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: maSignal.Rd:28: unexpected '}'
prepare_Rd: maSignal.Rd:1: All text must be in a section
prepare_Rd: maSignal.Rd:3: All text must be in a section
prepare_Rd: maSignal.Rd:5: All text must be in a section
prepare_Rd: maSignal.Rd:27: All text must be in a section
prepare_Rd: saveERCCPlots.Rd:104: unexpected '}'
prepare_Rd: saveERCCPlots.Rd:1: All text must be in a section
prepare_Rd: saveERCCPlots.Rd:3: All text must be in a section
prepare_Rd: saveERCCPlots.Rd:5: All text must be in a section
prepare_Rd: saveERCCPlots.Rd:103: All text must be in a section
* 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 ... WARNING
Warning: parse error in file 'erccdashboard-Ex.R':
273:1: unexpected input
272:
273: <<
^
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ‘erccdashboard-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: maSignal
> ### Title: Generate MA plots with or without annotation using LODR
> ### estimates
> ### Aliases: maSignal
>
> ### ** Examples
>
> <<<<<<< HEAD
Error: unexpected input in "<<"
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, 3 WARNINGs, 1 NOTE
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00check.log’
for details.
* installing *source* package ‘erccdashboard’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/maSignal.Rd:28: unexpected '}'
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/maSignal.Rd:1: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/maSignal.Rd:3: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/maSignal.Rd:5: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/maSignal.Rd:27: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/saveERCCPlots.Rd:104: unexpected '}'
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/saveERCCPlots.Rd:1: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/saveERCCPlots.Rd:3: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/saveERCCPlots.Rd:5: All text must be in a section
Warning: /Users/biocbuild/bbs-3.4-bioc/meat/erccdashboard.Rcheck/00_pkg_src/erccdashboard/man/saveERCCPlots.Rd:103: All text must be in a section
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (erccdashboard)