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BioC 3.2: CHECK report for MiRaGE on perceval

This page was generated on 2015-11-10 14:47:33 -0800 (Tue, 10 Nov 2015).

Package 649/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MiRaGE 1.12.0
Y-h. Taguchi
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/MiRaGE
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: MiRaGE
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MiRaGE_1.12.0.tar.gz
StartedAt: 2015-11-10 07:05:18 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 07:07:03 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 105.3 seconds
RetCode: 0
Status:  OK 
CheckDir: MiRaGE.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 MiRaGE_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MiRaGE.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 ‘MiRaGE/DESCRIPTION’ ... OK
* this is package ‘MiRaGE’ version ‘1.12.0’
* 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:
  vignettes/.goutputstream-0CTGCW
  vignettes/.goutputstream-E9SXCW
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 ... [8s/8s] OK
* 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
* 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' call to ‘miRNATarget’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘Biobase’
  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
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’
HS_conv_id: no visible global function definition for ‘read.fasta’
id_conv_gen: no visible global function definition for ‘useMart’
id_conv_gen: no visible global function definition for ‘listDatasets’
id_conv_gen: no visible global function definition for ‘useDataset’
id_conv_gen: no visible global function definition for ‘listAttributes’
id_conv_gen: no visible global function definition for ‘getBM’
MiRaGEAnalysis: no visible global function definition for ‘fData’
MiRaGEAnalysis: no visible global function definition for ‘exprs’
MiRaGEAnalysis: no visible global function definition for ‘pData’
MM_conv_id: no visible global function definition for ‘read.fasta’
TBL2_HS_gen: no visible global function definition for
  ‘makeTxDbFromUCSC’
TBL2_HS_gen: no visible global function definition for
  ‘threeUTRsByTranscript’
TBL2_HS_gen: no visible global function definition for ‘getSeq’
TBL2_HS_gen: no visible binding for global variable ‘Hsapiens’
TBL2_HS_gen: no visible global function definition for ‘elementLengths’
TBL2_HS_gen: no visible global function definition for ‘write.fasta’
TBL2_HS_gen: no visible binding for global variable ‘s2c’
TBL2_HS_gen: no visible global function definition for
  ‘readDNAStringSet’
TBL2_HS_gen: no visible global function definition for
  ‘readRNAStringSet’
TBL2_HS_gen: no visible global function definition for ‘subseq’
TBL2_HS_gen: no visible global function definition for ‘DNAString’
TBL2_HS_gen: no visible global function definition for ‘RNAString’
TBL2_HS_gen: no visible global function definition for
  ‘reverseComplement’
TBL2_HS_gen: no visible global function definition for ‘vcountPattern’
TBL2_MM_gen: no visible global function definition for
  ‘makeTxDbFromUCSC’
TBL2_MM_gen: no visible global function definition for
  ‘threeUTRsByTranscript’
TBL2_MM_gen: no visible global function definition for ‘getSeq’
TBL2_MM_gen: no visible binding for global variable ‘Mmusculus’
TBL2_MM_gen: no visible global function definition for ‘elementLengths’
TBL2_MM_gen: no visible global function definition for ‘write.fasta’
TBL2_MM_gen: no visible binding for global variable ‘s2c’
TBL2_MM_gen: no visible global function definition for
  ‘readDNAStringSet’
TBL2_MM_gen: no visible global function definition for
  ‘readRNAStringSet’
TBL2_MM_gen: no visible global function definition for ‘subseq’
TBL2_MM_gen: no visible global function definition for ‘DNAString’
TBL2_MM_gen: no visible global function definition for ‘RNAString’
TBL2_MM_gen: no visible global function definition for
  ‘reverseComplement’
TBL2_MM_gen: no visible global function definition for ‘vcountPattern’
* 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 ... [22s/22s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
MiRaGE        10.961  2.146  13.172
getMiRaGEData  4.602  0.651   5.253
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/MiRaGE.Rcheck/00check.log’
for details.


MiRaGE.Rcheck/00install.out:

* installing *source* package ‘MiRaGE’ ...
** 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 (MiRaGE)

MiRaGE.Rcheck/MiRaGE-Ex.timings:

nameusersystemelapsed
HS_conv_id0.0010.0000.000
MM_conv_id000
MiRaGE10.961 2.14613.172
TBL2_HS_gen0.0010.0000.001
TBL2_MM_gen0.0000.0000.001
getMiRaGEData4.6020.6515.253
id_conv_gen0.0000.0000.001