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CHECK report for MiRaGE on merida2

This page was generated on 2018-10-17 08:50:31 -0400 (Wed, 17 Oct 2018).

Package 913/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MiRaGE 1.22.0
Y-h. Taguchi
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/MiRaGE
Branch: RELEASE_3_7
Last Commit: c600291
Last Changed Date: 2018-04-30 10:35:25 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MiRaGE
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MiRaGE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MiRaGE_1.22.0.tar.gz
StartedAt: 2018-10-16 22:40:37 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 22:42:13 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 95.7 seconds
RetCode: 0
Status:  OK 
CheckDir: MiRaGE.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MiRaGE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MiRaGE_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MiRaGE.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MiRaGE/DESCRIPTION’ ... OK
* this is package ‘MiRaGE’ version ‘1.22.0’
* 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 ... 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 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.
Missing or unexported object: ‘IRanges::unlist’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
HS_conv_id: no visible global function definition for ‘download.file’
HS_conv_id: no visible global function definition for ‘read.fasta’
HS_conv_id: no visible global function definition for ‘read.csv’
MM_conv_id: no visible global function definition for ‘download.file’
MM_conv_id: no visible global function definition for ‘read.fasta’
MM_conv_id: no visible global function definition for ‘read.csv’
MiRaGEAnalysis: no visible global function definition for ‘fData’
MiRaGEAnalysis: no visible global function definition for ‘exprs’
MiRaGEAnalysis: no visible global function definition for ‘pData’
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 ‘write.fasta’
TBL2_HS_gen: no visible binding for global variable ‘s2c’
TBL2_HS_gen: no visible global function definition for ‘download.file’
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 ‘write.fasta’
TBL2_MM_gen: no visible binding for global variable ‘s2c’
TBL2_MM_gen: no visible global function definition for ‘download.file’
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’
getMiRaGEData: no visible global function definition for ‘biocLite’
getMiRaGEData: no visible global function definition for ‘data’
getMiRaGEData: no visible binding for global variable ‘TBL2_MM’
getMiRaGEData: no visible binding for global variable ‘TBL2’
getMiRaGEData: no visible binding for global variable ‘TBL2_HS’
getMiRaGEData: no visible binding for global variable ‘id_conv’
getMiRaGEData: no visible binding for global variable ‘conv_id’
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 ‘write.table’
id_conv_gen: no visible global function definition for ‘read.csv’
id_conv_gen: no visible global function definition for ‘getBM’
Undefined global functions or variables:
  DNAString Hsapiens Mmusculus RNAString TBL2 TBL2_HS TBL2_MM biocLite
  conv_id data download.file exprs fData getBM getSeq id_conv
  listAttributes listDatasets makeTxDbFromUCSC pData read.csv
  read.fasta readDNAStringSet readRNAStringSet reverseComplement s2c
  subseq threeUTRsByTranscript useDataset useMart vcountPattern
  write.fasta write.table
Consider adding
  importFrom("utils", "data", "download.file", "read.csv", "write.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
MiRaGE        8.962  1.849  10.894
getMiRaGEData 4.535  0.643   5.302
* 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-3.7-bioc/meat/MiRaGE.Rcheck/00check.log’
for details.



Installation output

MiRaGE.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MiRaGE
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MiRaGE’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MiRaGE)

Tests output


Example timings

MiRaGE.Rcheck/MiRaGE-Ex.timings

nameusersystemelapsed
HS_conv_id0.0000.0000.001
MM_conv_id0.0010.0000.002
MiRaGE 8.962 1.84910.894
TBL2_HS_gen0.0010.0000.001
TBL2_MM_gen0.0010.0000.001
getMiRaGEData4.5350.6435.302
id_conv_gen0.0010.0000.001