RmiR 1.34.0
Francesco Favero
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/RmiR |
| Branch: RELEASE_3_6 |
| Last Commit: 5c39f7d |
| Last Changed Date: 2017-10-30 12:39:26 -0400 (Mon, 30 Oct 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf RmiR.buildbin-libdir RmiR.Rcheck && mkdir RmiR.buildbin-libdir RmiR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RmiR.buildbin-libdir RmiR_1.34.0.tar.gz >RmiR.Rcheck\00install.out 2>&1 && cp RmiR.Rcheck\00install.out RmiR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RmiR.buildbin-libdir --install="check:RmiR-install.out" --force-multiarch --no-vignettes --timings RmiR_1.34.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RmiR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.34.0'
* 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 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 installed files from 'inst/doc' ... 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 16.13 0.54 39.38
plotRmiRtc 8.28 0.14 8.47
RmiRtc 8.23 0.10 8.32
** 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, cbind, colMeans, colSums, colnames, 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
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-3.6-bioc/meat/RmiR.Rcheck/00check.log'
for details.