[Bioc-devel] Errors in recent updates of MiRaGE development release

Dan Tenenbaum dtenenba at fhcrc.org
Tue Dec 10 04:10:51 CET 2013 


----- Original Message -----
> From: "Y-h. Taguchi" <tag at granular.com>
> To: bioc-devel at r-project.org
> Sent: Monday, December 9, 2013 6:04:20 PM
> Subject: [Bioc-devel] Errors in recent updates of MiRaGE development release
> 
> Dear Maintainers,
> 
> Thank you very much for your every efforts to maintain this fantastic
> project!
> 
> By the way, today I would like to ask you to solve the recent issues
> raised for the  recent update of my Package, MiRaGE.
> http://www.bioconductor.org/checkResults/devel/bioc-LATEST/MiRaGE/zin2-buildsrc.html
> Although there were some Errors reported to mine, I believe that this
> is not the problem on my packages but your system because of the
> following reasons.
> 
> I am also happy if some one else can advise me on how to resolve this
> problem!
> 
> Reason 1:
> At first, I have faced the very same problem on my Linux box, but
> this
> problem was resolved immediately resolved after simply re-installing
> R
> itself from the scratch (i.e., recompiling from the source code, I
> used ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz)
> 
> Reason 2:
> This error was reported to be "error reading from connection" that
> was
> also known to be often resolved after re-installing R from the
> scratch.
> (sorry this information source is written in Japanese. I can not show
> it to you)
> 
> Reason 3:
> In my local linux box, MiRaGE can pass R CMD check
> (see attached in the followings)
> 
> Reason 4:
> In my local linux box, ‘MiRaGE_1.5.2.tar.gz’ can be constructed
> successfully without any problems after simple re-installing R from
> the scratch.
> (see attached in the following)
> 
> Reason 5:
> I used vary similar linux system (Ubuntu 12.04 LTS)  to those used in
> your system
> (see also attached in the following)
> 
> Reason 6:
> Since "svn status MiRaGE" does not return anything, I think that
> there
> are no differences between uploaded one and local one.
> 
> Thank you very much for your supporting.
> 
> yours, tag.


The problem is not with your code but with this URL:

http://granular.com/MiRaGE/DATA2/TBL2_HS

Apparently some of the time it returns an error. This is why the package built and checked on Windows but not on the other platforms, and why neither you nor I can consistently reproduce the problem.

Dan


> 
> =========== output from R build ====
>  % ~/R-devel/bin/R CMD build --resave-data MiRaGE
> * checking for file ‘MiRaGE/DESCRIPTION’ ... OK
> * preparing ‘MiRaGE’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * looking to see if a ‘data/datalist’ file should be added
> * re-saving image files
> * building ‘MiRaGE_1.5.2.tar.gz’
> ==================== 00check.log ================
> * using log directory
> ‘/home/tag/RESEARCH/BioConductor_submit_new/MiRaGE.Rcheck’
> * using R Under development (unstable) (2013-12-05 r64395)
> * using platform: x86_64-unknown-linux-gnu (64-bit)
> * using session charset: UTF-8
> * checking for file ‘MiRaGE/DESCRIPTION’ ... OK
> * this is package ‘MiRaGE’ version ‘1.5.2’
> * 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 executable files ... OK
> * checking for hidden files and directories ... NOTE
> Found the following hidden files and directories:
>   vignettes/.goutputstream-0CTGCW
>   vignettes/.goutputstream-E9SXCW
>   vignettes/.svn/text-base/.goutputstream-0CTGCW.svn-base
>   vignettes/.svn/text-base/.goutputstream-E9SXCW.svn-base
>   .svn
>   R/.svn
>   data/.svn
>   inst/.svn
>   inst/extdata/.svn
>   man/.svn
>   vignettes/.svn
> These were most likely included in error. See section ‘Package
> structure’ in the ‘Writing R Extensions’ manual.
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking whether package ‘MiRaGE’ can be installed ... OK
> * checking installed package size ... OK
> * checking package 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
> * 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 dependencies in R code ... NOTE
> Package in Depends field not imported from: ‘Biobase’
>   These packages need to be imported from for the case when
>   this namespace is loaded but not attached.
> See the information on DESCRIPTION files in the chapter ‘Creating R
> packages’ of the ‘Writing R Extensions’ manual.
> * checking S3 generic/method consistency ... OK
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... NOTE
> getMiRaGEData: no visible global function definition for ‘biocLite’
> getMiRaGEData: no visible binding for global variable ‘TBL2’
> getMiRaGEData: no visible binding for global variable ‘id_conv’
> getMiRaGEData: no visible binding for global variable ‘conv_id’
> * 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 files in ‘vignettes’ ... OK
> * checking examples ... OK
> * checking for unstated dependencies in vignettes ... OK
> * checking package vignettes in ‘inst/doc’ ... WARNING
> Package vignette without corresponding PDF/HTML:
>    ‘MiRaGE.Rnw’
> 
> * checking running R code from vignettes ... OK
> * checking re-building of vignette outputs ... OK
> * checking PDF version of manual ... OK
> WARNING: There was 1 warning.
> NOTE: There were 3 notes.
> ====== sessionInfo() =====
> % ~/R-devel/bin/R
> 
> R Under development (unstable) (2013-12-05 r64395) -- "Unsuffered
> Consequences"
> Copyright (C) 2013 The R Foundation for Statistical Computing
> Platform: x86_64-unknown-linux-gnu (64-bit)
> .
> .
> .
> .
> 
> > sessionInfo()
> R Under development (unstable) (2013-12-05 r64395)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=ja_JP.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=ja_JP.UTF-8        LC_COLLATE=ja_JP.UTF-8
>  [5] LC_MONETARY=ja_JP.UTF-8    LC_MESSAGES=ja_JP.UTF-8
>  [7] LC_PAPER=ja_JP.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=ja_JP.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
> --
> Y-h. Taguchi, Dept. Phys., Chuo Univ., Kasuga, Bunkyo-ku, Tokyo
> 112-8551,Japan
> Tel./Fax.  +81-3-3817-1791/1792
>  http://www.granular.com/tag/index-j.html
> 〒112-8551 中央大学理工学部 物理学科 田口善弘 電話/FAX 03-3817-1791/1792
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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>

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