Y-h. Taguchi
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/MiRaGE |
| Branch: RELEASE_3_6 |
| Last Commit: 3876ff0 |
| Last Changed Date: 2017-10-30 12:39:41 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:35:36 -0400 (Thu, 12 Apr 2018).
| Package 863/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MiRaGE 1.20.0 Y-h. Taguchi
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: MiRaGE |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MiRaGE_1.20.0.tar.gz |
| StartedAt: 2018-04-12 06:30:13 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 06:31:47 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 94.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MiRaGE.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MiRaGE_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MiRaGE.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.20.0’
* 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:
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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MiRaGE 7.361 1.443 8.959
* 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-3.6-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
| name | user | system | elapsed | |
| HS_conv_id | 0 | 0 | 0 | |
| MM_conv_id | 0 | 0 | 0 | |
| MiRaGE | 7.361 | 1.443 | 8.959 | |
| TBL2_HS_gen | 0.000 | 0.000 | 0.001 | |
| TBL2_MM_gen | 0.000 | 0.000 | 0.001 | |
| getMiRaGEData | 3.741 | 0.500 | 4.333 | |
| id_conv_gen | 0.001 | 0.000 | 0.000 | |