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

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List:       bioc-devel
Subject:    Re: [Bioc-devel] Errors in recent updates of MiRaGE development release
From:       Dan Tenenbaum <dtenenba () fhcrc ! org>
Date:       2013-12-10 3:10:51
Message-ID: 896919617.325803.1386645051732.JavaMail.root () fhcrc ! org
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----- Original Message -----
> From: "Y-h. Taguchi" <tag@granular.com>
> To: bioc-devel@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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 

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