GSE62944 1.1.2
Bioconductor Package Maintainer
| Snapshot Date: 2016-09-17 09:20:18 -0700 (Sat, 17 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/GSE62944 | | Last Changed Rev: 3826 / Revision: 3889 | | Last Changed Date: 2016-07-14 11:58:00 -0700 (Thu, 14 Jul 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GSE62944_1.1.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/GSE62944.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSE62944/DESCRIPTION’ ... OK
* this is package ‘GSE62944’ version ‘1.1.2’
* 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 ‘GSE62944’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Found directory ‘R’ with no source files.
* 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 ... NOTE
Error in tools:::.check_packages_used(package = "GSE62944") :
directory '/home/biocbuild/bbs-3.4-data-experiment/meat/GSE62944.Rcheck/GSE62944' does not contain R code
Execution halted
* checking S3 generic/method consistency ... WARNING
Error in tools::checkS3methods(package = "GSE62944") :
directory '/home/biocbuild/bbs-3.4-data-experiment/meat/GSE62944.Rcheck/GSE62944' does not contain R code
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error in tools::checkReplaceFuns(package = "GSE62944") :
directory '/home/biocbuild/bbs-3.4-data-experiment/meat/GSE62944.Rcheck/GSE62944' does not contain R code
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error in tools::checkFF(package = "GSE62944", registration = FALSE, check_DUP = TRUE) :
directory '/home/biocbuild/bbs-3.4-data-experiment/meat/GSE62944.Rcheck/GSE62944' does not contain R code
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Error in tools::codoc(package = "GSE62944") :
directory '/home/biocbuild/bbs-3.4-data-experiment/meat/GSE62944.Rcheck/GSE62944' does not contain R code
Execution halted
Error in tools::codocClasses(package = "GSE62944") :
directory '/home/biocbuild/bbs-3.4-data-experiment/meat/GSE62944.Rcheck/GSE62944' does not contain R code
Execution halted
* checking Rd \usage sections ... NOTE
Error in tools::checkDocStyle(package = "GSE62944") :
directory '/home/biocbuild/bbs-3.4-data-experiment/meat/GSE62944.Rcheck/GSE62944' does not contain R code
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
Warning: parse error in file 'GSE62944-Ex.R':
24:28: unexpected string constant
23: x
24: y <- query(hub, "GSE62944" "se"
^
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GSE62944-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GSE62944-package
> ### Title: GEO accession GSE62944 available as an 'ExpressionSet' object.
> ### Aliases: GSE62944-package GSE62944
> ### Keywords: utilities
>
> ### ** Examples
>
> library(ExperimentHub)
Loading required package: AnnotationHub
Attaching package: ‘AnnotationHub’
The following object is masked from ‘package:Biobase’:
cache
> hub <- ExperimentHub()
snapshotDate(): 2016-08-08
> x <- query(hub, "GSE62944", "se", "tumor")
> x
ExperimentHub with 3 records
# snapshotDate(): 2016-08-08
# $dataprovider: GEO
# $species: Homo sapiens
# $rdataclass: SummarizedExperiment, ExpressionSet
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# sourceurl, sourcetype
# retrieve records with, e.g., 'object[["EH1"]]'
title
EH1 | RNA-Sequencing and clinical data for 7706 tumor samples from The...
EH164 | RNA-Sequencing and clinical data for 9246 tumor samples from The...
EH165 | RNA-Sequencing and clinical data for 741 normal samples from The...
> y <- query(hub, "GSE62944" "se", "normal")
Error: unexpected string constant in "y <- query(hub, "GSE62944" "se""
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘DESeq2’
* 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, 5 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.4-data-experiment/meat/GSE62944.Rcheck/00check.log’
for details.