anamiR 1.2.4
Ti-Tai Wang
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/anamiR | | Last Changed Rev: 128985 / Revision: 129046 | | Last Changed Date: 2017-04-20 18:47:13 -0400 (Thu, 20 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | ERROR | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | ERROR | skipped | skipped | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ ERROR ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / 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 anamiR_1.2.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/anamiR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘anamiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘anamiR’ version ‘1.2.4’
* 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 ‘anamiR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 20.7Mb
sub-directories of 1Mb or more:
extdata 19.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘SummarizedExperiment’
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 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
GSEA_ana: no visible binding for global variable ‘msigdb.gs’
Undefined global functions or variables:
msigdb.gs
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘table_pre’
Undocumented data sets:
‘table_pre’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ‘anamiR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GSEA_ana
> ### Title: This function will do GSEA analysis.
> ### Aliases: GSEA_ana
>
> ### ** Examples
>
>
> require(data.table)
Loading required package: data.table
Attaching package: ‘data.table’
The following object is masked from ‘package:SummarizedExperiment’:
shift
The following object is masked from ‘package:GenomicRanges’:
shift
The following object is masked from ‘package:IRanges’:
shift
The following objects are masked from ‘package:S4Vectors’:
first, second
>
> ## Load example data
> aa <- system.file("extdata", "GSE19536_mrna.csv", package = "anamiR")
> mrna <- fread(aa, fill = TRUE, header = TRUE)
>
> bb <- system.file("extdata", "GSE19536_mirna.csv", package = "anamiR")
> mirna <- fread(bb, fill = TRUE, header = TRUE)
>
> cc <- system.file("extdata", "pheno_data.csv", package = "anamiR")
> pheno.data <- fread(cc, fill = TRUE, header = TRUE)
>
> ## adjust data format
> mirna_name <- mirna[["miRNA"]]
> mrna_name <- mrna[["Gene"]]
> mirna <- mirna[, -1]
> mrna <- mrna[, -1]
> mirna <- data.matrix(mirna)
> mrna <- data.matrix(mrna)
> row.names(mirna) <- mirna_name
> row.names(mrna) <- mrna_name
> pheno_name <- pheno.data[["Sample"]]
> pheno.data <- pheno.data[, -1]
> pheno.data <- as.matrix(pheno.data)
> row.names(pheno.data) <- pheno_name
>
> ## SummarizedExperiment class
> require(SummarizedExperiment)
> mirna_se <- SummarizedExperiment(
+ assays = SimpleList(counts=mirna),
+ colData = pheno.data)
>
> mrna_se <- SummarizedExperiment(
+ assays = SimpleList(counts=mrna),
+ colData = pheno.data)
>
> table <- GSEA_ana(mrna_se = mrna_se,
+ mirna_se = mirna_se, class = "ER",
+ pathway_num = 2)
Error in saaTest(exprs, gsets = gsets, set.size = set.size, same.dir = same.dir) :
object 'msigdb.gs' not found
Calls: GSEA_ana -> <Anonymous> -> saaTest
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, 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/anamiR.Rcheck/00check.log’
for details.