MiRaGE 1.16.0
Y-h. Taguchi
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/MiRaGE | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf MiRaGE.buildbin-libdir MiRaGE.Rcheck && mkdir MiRaGE.buildbin-libdir MiRaGE.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MiRaGE.buildbin-libdir MiRaGE_1.16.0.tar.gz >MiRaGE.Rcheck\00install.out 2>&1 && cp MiRaGE.Rcheck\00install.out MiRaGE-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MiRaGE.buildbin-libdir --install="check:MiRaGE-install.out" --force-multiarch --no-vignettes --timings MiRaGE_1.16.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/MiRaGE.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.16.0'
* 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 6.86 0.83 8.88
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MiRaGE 7.68 0.46 8.12
* 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-3.4-bioc/meat/MiRaGE.Rcheck/00check.log'
for details.
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_1.16.0.zip
* DONE (MiRaGE)