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This page was generated on 2021-09-17 15:05:45 -0400 (Fri, 17 Sep 2021).

CHECK results for MiRaGE on nebbiolo1

To the developers/maintainers of the MiRaGE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MiRaGE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1145/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MiRaGE 1.34.0  (landing page)
Y-h. Taguchi
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/MiRaGE
git_branch: RELEASE_3_13
git_last_commit: 726e7d4
git_last_commit_date: 2021-05-19 11:52:32 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MiRaGE
Version: 1.34.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MiRaGE.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MiRaGE_1.34.0.tar.gz
StartedAt: 2021-09-16 10:36:17 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 10:37:55 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 97.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MiRaGE.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MiRaGE.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MiRaGE_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MiRaGE.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MiRaGE/DESCRIPTION’ ... OK
* this is package ‘MiRaGE’ version ‘1.34.0’
* 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 ... WARNING
'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
  ‘install.packages’
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 conv_id
  data download.file exprs fData getBM getSeq id_conv install.packages
  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", "install.packages",
             "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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
MiRaGE 6.178  0.728   6.912
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/MiRaGE.Rcheck/00check.log’
for details.



Installation output

MiRaGE.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MiRaGE
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘MiRaGE’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MiRaGE)

Tests output


Example timings

MiRaGE.Rcheck/MiRaGE-Ex.timings

nameusersystemelapsed
HS_conv_id0.0010.0000.000
MM_conv_id000
MiRaGE6.1780.7286.912
TBL2_HS_gen000
TBL2_MM_gen0.0000.0010.000
getMiRaGEData2.9650.4353.400
id_conv_gen000