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BioC 3.2: CHECK report for TDARACNE on perceval

This page was generated on 2015-11-10 14:46:51 -0800 (Tue, 10 Nov 2015).

Package 1047/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TDARACNE 1.20.0
Zoppoli Pietro
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/TDARACNE
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TDARACNE
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TDARACNE_1.20.0.tar.gz
StartedAt: 2015-11-10 10:08:39 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 10:09:42 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 63.5 seconds
RetCode: 0
Status:  OK 
CheckDir: TDARACNE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TDARACNE_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TDARACNE.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TDARACNE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TDARACNE’ version ‘1.20.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
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 ‘TDARACNE’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  inst/CITATION.txt
Most likely ‘inst/CITATION’ should be used instead.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘Biobase’ ‘GenKern’ ‘Rgraphviz’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘GenKern’ ‘Rgraphviz’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CalcMI_time2: no visible global function definition for ‘dpik’
CalcMI_time2: no visible global function definition for ‘KernSec’
CalcMI_time2: no visible global function definition for ‘KernSur’
TDARACNE: no visible global function definition for ‘exprs’
TDARACNEdataPublished: no visible binding for global variable
  ‘dataYeast’
TDARACNEdataPublished: no visible binding for global variable
  ‘threshYeast’
TDARACNEdataPublished: no visible binding for global variable
  ‘dataSOSmean’
TDARACNEdataPublished: no visible binding for global variable
  ‘threshSOSmean’
TDARACNEdataPublished: no visible binding for global variable
  ‘dataIRMAon’
TDARACNEdataPublished: no visible binding for global variable
  ‘threshIRMAon’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
TDARACNEdataPublished 18.465  0.056  18.553
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/TDARACNE.Rcheck/00check.log’
for details.


TDARACNE.Rcheck/00install.out:

* installing *source* package ‘TDARACNE’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TDARACNE)

TDARACNE.Rcheck/TDARACNE-Ex.timings:

nameusersystemelapsed
TDARACNE2.5180.0262.544
TDARACNEdataPublished18.465 0.05618.553