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BioC 3.5: CHECK report for MiRaGE on tokay2

This page was generated on 2017-08-16 13:21:41 -0400 (Wed, 16 Aug 2017).

Package 825/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MiRaGE 1.18.0
Y-h. Taguchi
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MiRaGE
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MiRaGE
Version: 1.18.0
Command: rm -rf MiRaGE.buildbin-libdir MiRaGE.Rcheck && mkdir MiRaGE.buildbin-libdir MiRaGE.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MiRaGE.buildbin-libdir MiRaGE_1.18.0.tar.gz >MiRaGE.Rcheck\00install.out 2>&1 && cp MiRaGE.Rcheck\00install.out MiRaGE-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MiRaGE.buildbin-libdir --install="check:MiRaGE-install.out" --force-multiarch --no-vignettes --timings MiRaGE_1.18.0.tar.gz
StartedAt: 2017-08-16 01:17:00 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:19:19 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 139.6 seconds
RetCode: 0
Status:  OK  
CheckDir: MiRaGE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MiRaGE.buildbin-libdir MiRaGE.Rcheck && mkdir MiRaGE.buildbin-libdir MiRaGE.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MiRaGE.buildbin-libdir MiRaGE_1.18.0.tar.gz >MiRaGE.Rcheck\00install.out 2>&1 && cp MiRaGE.Rcheck\00install.out MiRaGE-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MiRaGE.buildbin-libdir --install="check:MiRaGE-install.out" --force-multiarch --no-vignettes --timings MiRaGE_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MiRaGE.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MiRaGE/DESCRIPTION' ... OK
* this is package 'MiRaGE' version '1.18.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
MiRaGE 9.25    0.8   10.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
MiRaGE 5.25   0.63    5.88
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MiRaGE.Rcheck/00check.log'
for details.


MiRaGE.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'MiRaGE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MiRaGE' as MiRaGE_1.18.0.zip
* DONE (MiRaGE)

MiRaGE.Rcheck/examples_i386/MiRaGE-Ex.timings:

nameusersystemelapsed
HS_conv_id000
MM_conv_id000
MiRaGE 9.25 0.8010.33
TBL2_HS_gen000
TBL2_MM_gen000
getMiRaGEData3.910.344.25
id_conv_gen000

MiRaGE.Rcheck/examples_x64/MiRaGE-Ex.timings:

nameusersystemelapsed
HS_conv_id000
MM_conv_id000
MiRaGE5.250.635.88
TBL2_HS_gen000
TBL2_MM_gen000
getMiRaGEData1.980.302.28
id_conv_gen000