[Bioc-devel] Errors in recent updates of MiRaGE development release
Y-h. Taguchi
tag at granular.com
Tue Dec 10 03:04:20 CET 2013
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.
=========== 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
More information about the Bioc-devel
mailing list