maSigPro 1.48.0
Maria Jose Nueda
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/maSigPro | | Branch: RELEASE_3_5 | | Last Commit: e5508c4 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK |  |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | 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 maSigPro_1.48.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/maSigPro.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 ‘maSigPro/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maSigPro’ version ‘1.48.0’
* 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 ‘maSigPro’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’ ‘stats’ ‘MASS’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘utils’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ‘maSigPro-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: see.genes
> ### Title: Wrapper function for visualization of gene expression values of
> ### time course experiments
> ### Aliases: see.genes
> ### Keywords: manip aplot
>
> ### ** Examples
>
>
> #### GENERATE TIME COURSE DATA
> ## generate n random gene expression profiles of a data set with
> ## one control plus 3 treatments, 3 time points and r replicates per time point.
>
> tc.GENE <- function(n, r,
+ var11 = 0.01, var12 = 0.01,var13 = 0.01,
+ var21 = 0.01, var22 = 0.01, var23 =0.01,
+ var31 = 0.01, var32 = 0.01, var33 = 0.01,
+ var41 = 0.01, var42 = 0.01, var43 = 0.01,
+ a1 = 0, a2 = 0, a3 = 0, a4 = 0,
+ b1 = 0, b2 = 0, b3 = 0, b4 = 0,
+ c1 = 0, c2 = 0, c3 = 0, c4 = 0)
+ {
+
+ tc.dat <- NULL
+ for (i in 1:n) {
+ Ctl <- c(rnorm(r, a1, var11), rnorm(r, b1, var12), rnorm(r, c1, var13)) # Ctl group
+ Tr1 <- c(rnorm(r, a2, var21), rnorm(r, b2, var22), rnorm(r, c2, var23)) # Tr1 group
+ Tr2 <- c(rnorm(r, a3, var31), rnorm(r, b3, var32), rnorm(r, c3, var33)) # Tr2 group
+ Tr3 <- c(rnorm(r, a4, var41), rnorm(r, b4, var42), rnorm(r, c4, var43)) # Tr3 group
+ gene <- c(Ctl, Tr1, Tr2, Tr3)
+ tc.dat <- rbind(tc.dat, gene)
+ }
+ tc.dat
+ }
>
> ## Create 270 flat profiles
> flat <- tc.GENE(n = 270, r = 3)
Failed to connect to Mir: Failed to connect to server socket: No such file or directory
Unable to init server: Could not connect: Connection refused
Error: cannot open display: :1.0
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: iceweasel: not found
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: seamonkey: not found
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: mozilla: not found
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: epiphany: not found
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: konqueror: not found
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: chromium-browser: not found
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: google-chrome: not found
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: www-browser: not found
> ## Create 10 genes with profile differences between Ctl and Tr1 groups
> twodiff <- tc.GENE (n = 10, r = 3, b2 = 0.5, c2 = 1.3)
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: links2: not found
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: elinks: not found
> ## Create 10 genes with profile differences between Ctl, Tr2, and Tr3 groups
> threediff <- tc.GENE(n = 10, r = 3, b3 = 0.8, c3 = -1, a4 = -0.1, b4 = -0.8, c4 = -1.2)
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: links: not found
> ## Create 10 genes with profile differences between Ctl and Tr2 and different variance
> vardiff <- tc.GENE(n = 10, r = 3, a3 = 0.7, b3 = 1, c3 = 1.2, var32 = 0.03, var33 = 0.03)
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: lynx: not found
/usr/bin/xdg-open: 771: /usr/bin/xdg-open: w3m: not found
xdg-open: no method available for opening '/home/biocbuild/bbs-3.5-bioc/meat/maSigPro.Rcheck/maSigPro/doc/maSigProUsersGuide.pdf'
> ## Create dataset
> tc.DATA <- rbind(flat, twodiff, threediff, vardiff)
> rownames(tc.DATA) <- paste("feature", c(1:300), sep = "")
> colnames(tc.DATA) <- paste("Array", c(1:36), sep = "")
> tc.DATA [sample(c(1:(300*36)), 300)] <- NA # introduce missing values
>
> #### CREATE EXPERIMENTAL DESIGN
> Time <- rep(c(rep(c(1:3), each = 3)), 4)
> Replicates <- rep(c(1:12), each = 3)
> Control <- c(rep(1, 9), rep(0, 27))
> Treat1 <- c(rep(0, 9), rep(1, 9), rep(0, 18))
> Treat2 <- c(rep(0, 18), rep(1, 9), rep(0,9))
> Treat3 <- c(rep(0, 27), rep(1, 9))
> edesign <- cbind(Time, Replicates, Control, Treat1, Treat2, Treat3)
> rownames(edesign) <- paste("Array", c(1:36), sep = "")
>
> see.genes(tc.DATA, edesign = edesign, k = 4, main = "Time Course")
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: see.genes -> 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/maSigPro.Rcheck/00check.log’
for details.