Package: RmiR

Version: 1.38.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RmiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RmiR_1.38.0.tar.gz

StartedAt: 2019-04-13 05:05:39 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 05:09:24 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 225.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: RmiR.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RmiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RmiR_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RmiR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RmiR/DESCRIPTION' ... OK
* this is package 'RmiR' version '1.38.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'RmiR' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
'library' or 'require' call to 'RSVGTipsDevice' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RSVGTipsDevice' 'RmiR.Hs.miRNA'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotRmiRtc: no visible global function definition for 'devSVGTips'
plotRmiRtc: no visible global function definition for 'plot'
plotRmiRtc: no visible global function definition for
  'setSVGShapeToolTip'
plotRmiRtc: no visible global function definition for 'setSVGShapeURL'
plotRmiRtc: no visible global function definition for 'points'
plotRmiRtc: no visible global function definition for 'lines'
plotRmiRtc: no visible global function definition for 'legend'
plotRmiRtc: no visible global function definition for 'dev.off'
readRmiRtc: no visible global function definition for 'write.table'
Undefined global functions or variables:
  dev.off devSVGTips legend lines plot points setSVGShapeToolTip
  setSVGShapeURL write.table
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
RmiR       14.66   0.52   42.00
plotRmiRtc  8.24   0.07    8.31
RmiRtc      7.75   0.13    7.87
** running examples for arch 'x64' ... ERROR
Running examples in 'RmiR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotRmiRtc
> ### Title: Plot object from read.mir or a selected gene and respective
> ###   miRNAs from a miRtcList object
> ### Aliases: plotRmiRtc
> 
> ### ** Examples
> 
> 	
>         data(RmiR)
>         res1 <- read.mir(genes=gene1, mirna=mir1, annotation="hgug4112a.db")
Loading required package: hgug4112a.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: org.Hs.eg.db
>         res2 <- read.mir(genes=gene2, mirna=mir2, annotation="hgug4112a.db")
>         res3 <- read.mir(genes=gene3, mirna=mir3, annotation="hgug4112a.db")
> 
>         res_tc <- RmiRtc(timeline=c("res1", "res2", "res3"),
+ 			 timevalue=c(12, 48, 72))
>         res <- readRmiRtc(res_tc, correlation=-0.9, exprLev=1,
+ 			  annotation="hgug4112a.db")
> 
> 	## List of genes with anti-correlated miRNAs:
>         
> 	res$reps
  symbol miRNAs gene_id
2    APP      3     351
3  VLDLR      3    7436
1  CENPV      1  201161
> 
> 	## Plot of the first gene of the list:
> 	plotRmiRtc (res, gene_id=351, timeunit="Hours")
> 
> 	## Setting the position of the legend:
> 	
> 	plotRmiRtc (res,gene_id=351, legend.x=50, legend.y=0, timeunit="Hours")
> 
> 	## Plot with RSVGTipsDevice:
> 	
> 	plotRmiRtc (res,gene_id=351, legend.x=50, legend.y=0, timeunit="Hours",
+ 		    svgTips=TRUE)
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/RmiR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RmiR_1.38.0.tar.gz && rm -rf RmiR.buildbin-libdir && mkdir RmiR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RmiR.buildbin-libdir RmiR_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RmiR_1.38.0.zip && rm RmiR_1.38.0.tar.gz RmiR_1.38.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  154k  100  154k    0     0  3712k      0 --:--:-- --:--:-- --:--:-- 4078k

install for i386

* installing *source* package 'RmiR' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RmiR'
    finding HTML links ... done
    RmiR                                    html  
    RmiRtc                                  html  
    data                                    html  
    plotRmiRtc                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RmiR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RmiR' as RmiR_1.38.0.zip
* DONE (RmiR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RmiR' successfully unpacked and MD5 sums checked
In R CMD INSTALL