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BioC experimental data: CHECK report for GSE62944 on moscato1

This page was generated on 2016-09-21 21:57:29 -0700 (Wed, 21 Sep 2016).

Package 124/304HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSE62944 1.1.2
Bioconductor Package Maintainer
Snapshot Date: 2016-09-21 09:20:16 -0700 (Wed, 21 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 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ ERROR ] OK 

Summary

Package: GSE62944
Version: 1.1.2
Command: rm -rf GSE62944.buildbin-libdir GSE62944.Rcheck && mkdir GSE62944.buildbin-libdir GSE62944.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GSE62944.buildbin-libdir GSE62944_1.1.2.tar.gz >GSE62944.Rcheck\00install.out 2>&1 && cp GSE62944.Rcheck\00install.out GSE62944-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GSE62944.buildbin-libdir --install="check:GSE62944-install.out" --force-multiarch --no-vignettes --timings GSE62944_1.1.2.tar.gz
StartedAt: 2016-09-21 14:22:50 -0700 (Wed, 21 Sep 2016)
EndedAt: 2016-09-21 14:24:26 -0700 (Wed, 21 Sep 2016)
EllapsedTime: 95.5 seconds
RetCode: 1
Status:  ERROR  
CheckDir: GSE62944.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   rm -rf GSE62944.buildbin-libdir GSE62944.Rcheck && mkdir GSE62944.buildbin-libdir GSE62944.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GSE62944.buildbin-libdir GSE62944_1.1.2.tar.gz >GSE62944.Rcheck\00install.out 2>&1 && cp GSE62944.Rcheck\00install.out GSE62944-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GSE62944.buildbin-libdir --install="check:GSE62944-install.out" --force-multiarch --no-vignettes --timings GSE62944_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-data-experiment/meat/GSE62944.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Error in tools:::.check_packages_used(package = "GSE62944") : 
  directory 'D:/biocbld/bbs-3.4-data-experiment/meat/GSE62944.buildbin-libdir/GSE62944' does not contain R code
Execution halted
* checking S3 generic/method consistency ... WARNING
Error in tools::checkS3methods(package = "GSE62944") : 
  directory 'D:/biocbld/bbs-3.4-data-experiment/meat/GSE62944.buildbin-libdir/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 'D:/biocbld/bbs-3.4-data-experiment/meat/GSE62944.buildbin-libdir/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 'D:/biocbld/bbs-3.4-data-experiment/meat/GSE62944.buildbin-libdir/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 'D:/biocbld/bbs-3.4-data-experiment/meat/GSE62944.buildbin-libdir/GSE62944' does not contain R code
Execution halted
Error in tools::codocClasses(package = "GSE62944") : 
  directory 'D:/biocbld/bbs-3.4-data-experiment/meat/GSE62944.buildbin-libdir/GSE62944' does not contain R code
Execution halted
* checking Rd \usage sections ... NOTE
Error in tools::checkDocStyle(package = "GSE62944") : 
  directory 'D:/biocbld/bbs-3.4-data-experiment/meat/GSE62944.buildbin-libdir/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':
25:28: unexpected string constant
24: x
25: y <- query(hub, "GSE62944" "se"
                               ^
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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
** running examples for arch 'x64' ... 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: 2 ERRORs, 5 WARNINGs, 4 NOTEs
See
  'D:/biocbld/bbs-3.4-data-experiment/meat/GSE62944.Rcheck/00check.log'
for details.

GSE62944.Rcheck/00install.out:


install for i386

* installing *source* package 'GSE62944' ...
** inst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'GSE62944' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSE62944' as GSE62944_1.1.2.zip
* DONE (GSE62944)

GSE62944.Rcheck/examples_i386/GSE62944-Ex.timings:

nameusersystemelapsed

GSE62944.Rcheck/examples_x64/GSE62944-Ex.timings:

nameusersystemelapsed