mBPCR 1.30.0
P.M.V. Rancoita
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/mBPCR | | Branch: RELEASE_3_5 | | Last Commit: 33fac43 | | 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 | [ ERROR ] | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK |  |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings mBPCR_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/mBPCR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mBPCR/DESCRIPTION’ ... OK
* this is package ‘mBPCR’ version ‘1.30.0’
* 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 ‘mBPCR’ 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
* 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
estProfileWithMBPCRforOligoSnpSet: no visible global function
definition for ‘new’
estProfileWithMBPCRforOligoSnpSet: no visible global function
definition for ‘integerMatrix’
importCNData: no visible global function definition for ‘read.table’
plotEstProfile: no visible global function definition for ‘x11’
plotEstProfile: no visible global function definition for ‘plot’
plotEstProfile: no visible global function definition for ‘title’
plotEstProfile: no visible global function definition for ‘legend’
plotEstProfile: no visible global function definition for ‘points’
writeEstProfile: no visible global function definition for
‘write.table’
Undefined global functions or variables:
integerMatrix legend new plot points read.table title write.table x11
Consider adding
importFrom("grDevices", "x11")
importFrom("graphics", "legend", "plot", "points", "title")
importFrom("methods", "new")
importFrom("utils", "read.table", "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 ... ERROR
Running examples in ‘mBPCR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotEstProfile
> ### Title: Plot the estimated profile of copy number data
> ### Aliases: plotEstProfile
> ### Keywords: hplot print
>
> ### ** Examples
>
> ##import the 10K data of cell line REC
> data(rec10k)
> ##estimation of chromosomes 3 and 5
> results <- estProfileWithMBPCR(rec10k$SNPname, rec10k$Chromosome, rec10k$PhysicalPosition, rec10k$log2ratio, chrToBeAnalyzed=c(3,5), maxProbeNumber=2000)
Estimation of global parameters
Estimation of the profile of chromosome 3
Computation of log(A^0)
Computation of left and right recursions
Determination of PC Regression
Estimation of the profile of chromosome 5
Computation of log(A^0)
Computation of left and right recursions
Determination of PC Regression
> ##plot the corresponding estimated profiles
> plotEstProfile(sampleName='rec10k', rec10k$Chromosome, rec10k$PhysicalPosition, rec10k$log2ratio, chrToBePlotted=c(3,5), results$estPC, maxProbeNumber=2000)
Warning in x11() : unable to open connection to X11 display ''
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, :
unable to start device X11cairo
Calls: plotEstProfile -> x11
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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/mBPCR.Rcheck/00check.log’
for details.
* installing *source* package ‘mBPCR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (mBPCR)