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BioC 3.5: CHECK report for GEOsearch on tokay2

This page was generated on 2017-08-16 13:24:53 -0400 (Wed, 16 Aug 2017).

Package 553/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEOsearch 1.2.0
Zhicheng Ji
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/GEOsearch
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ ERROR ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GEOsearch
Version: 1.2.0
Command: rm -rf GEOsearch.buildbin-libdir GEOsearch.Rcheck && mkdir GEOsearch.buildbin-libdir GEOsearch.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GEOsearch.buildbin-libdir GEOsearch_1.2.0.tar.gz >GEOsearch.Rcheck\00install.out 2>&1 && cp GEOsearch.Rcheck\00install.out GEOsearch-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GEOsearch.buildbin-libdir --install="check:GEOsearch-install.out" --force-multiarch --no-vignettes --timings GEOsearch_1.2.0.tar.gz
StartedAt: 2017-08-16 00:07:34 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:10:49 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 194.8 seconds
RetCode: 1
Status:  ERROR  
CheckDir: GEOsearch.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GEOsearch.buildbin-libdir GEOsearch.Rcheck && mkdir GEOsearch.buildbin-libdir GEOsearch.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GEOsearch.buildbin-libdir GEOsearch_1.2.0.tar.gz >GEOsearch.Rcheck\00install.out 2>&1 && cp GEOsearch.Rcheck\00install.out GEOsearch-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GEOsearch.buildbin-libdir --install="check:GEOsearch-install.out" --force-multiarch --no-vignettes --timings GEOsearch_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GEOsearch.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GEOsearch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEOsearch' version '1.2.0'
* 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 'GEOsearch' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GEOsearch' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GEOsearch.Rcheck/00install.out' for details.
* 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 ... 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
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
KeyWordFreq: no visible global function definition for 'data'
KeyWordFreq: no visible global function definition for 'p.adjust'
KeyWordFreq : <anonymous>: no visible global function definition for
  'fisher.test'
TermAlias: no visible global function definition for 'data'
TermAlias: no visible binding for global variable 'database'
TermAlias : <anonymous>: no visible binding for global variable
  'database'
TermAlias : <anonymous>: no visible global function definition for
  'keys'
TermAlias : <anonymous>: no visible binding for global variable 'db'
TermAlias : <anonymous>: no visible global function definition for
  'select'
Undefined global functions or variables:
  data database db fisher.test keys p.adjust select
Consider adding
  importFrom("stats", "fisher.test", "p.adjust")
  importFrom("utils", "data")
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' ... ERROR
Running examples in 'GEOsearch-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BatchDownload
> ### Title: BatchDownload
> ### Aliases: BatchDownload
> 
> ### ** Examples
> 
> BatchDownload("GSM1274542")
Error in mygetURL(paste0(SRXlink, SRRname, "/")) : 
  failed to get URL after 3 tries:
  url: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX383/SRX383211/SRR1037682
/
  error: Illegal characters found in URL
Calls: BatchDownload -> findSRX -> strsplit -> mygetURL
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'GEOsearch-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BatchDownload
> ### Title: BatchDownload
> ### Aliases: BatchDownload
> 
> ### ** Examples
> 
> BatchDownload("GSM1274542")
Error in mygetURL(paste0(SRXlink, SRRname, "/")) : 
  failed to get URL after 3 tries:
  url: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX383/SRX383211/SRR1037682
/
  error: Illegal characters found in URL
Calls: BatchDownload -> findSRX -> strsplit -> mygetURL
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: 2 ERRORs, 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/GEOsearch.Rcheck/00check.log'
for details.

GEOsearch.Rcheck/00install.out:


install for i386

* installing *source* package 'GEOsearch' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'GEOsearch' is deprecated and will be removed from Bioconductor
  version 3.6

install for x64

* installing *source* package 'GEOsearch' ...
** testing if installed package can be loaded
Warning: Package 'GEOsearch' is deprecated and will be removed from Bioconductor
  version 3.6
* MD5 sums
packaged installation of 'GEOsearch' as GEOsearch_1.2.0.zip
* DONE (GEOsearch)

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

nameusersystemelapsed

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

nameusersystemelapsed