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 | |  |
| 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 | |
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### Running command:
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### 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
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* 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.
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)