Y-h. Taguchi
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MiRaGE |
| Branch: RELEASE_3_8 |
| Last Commit: 2fa16b0 |
| Last Changed Date: 2019-01-04 13:39:33 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:11 -0400 (Sat, 13 Apr 2019).
| Package 965/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MiRaGE 1.24.1 Y-h. Taguchi
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MiRaGE |
| Version: 1.24.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MiRaGE.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MiRaGE_1.24.1.tar.gz |
| StartedAt: 2019-04-13 03:50:50 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:53:32 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 162.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MiRaGE.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MiRaGE.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MiRaGE_1.24.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MiRaGE.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.24.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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
* 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 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
'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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MiRaGE 6.03 0.98 7.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MiRaGE 5.81 0.36 6.17
* 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-3.8-bioc/meat/MiRaGE.Rcheck/00check.log'
for details.
MiRaGE.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MiRaGE_1.24.1.tar.gz && rm -rf MiRaGE.buildbin-libdir && mkdir MiRaGE.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MiRaGE.buildbin-libdir MiRaGE_1.24.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MiRaGE_1.24.1.zip && rm MiRaGE_1.24.1.tar.gz MiRaGE_1.24.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 985k 100 985k 0 0 20.2M 0 --:--:-- --:--:-- --:--:-- 21.8M
install for i386
* installing *source* package 'MiRaGE' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MiRaGE'
finding HTML links ... done
HS_conv_id html
MM_conv_id html
MiRaGE html
TBL2_HS_gen html
TBL2_MM_gen html
gene_exp html
getMiRaGEData html
id_conv_gen html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'MiRaGE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MiRaGE' as MiRaGE_1.24.1.zip
* DONE (MiRaGE)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MiRaGE' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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MiRaGE.Rcheck/examples_i386/MiRaGE-Ex.timings
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MiRaGE.Rcheck/examples_x64/MiRaGE-Ex.timings
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