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CHECK report for microRNA on malbec2

This page was generated on 2018-10-17 08:22:31 -0400 (Wed, 17 Oct 2018).

Package 903/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microRNA 1.38.0
"James F. Reid"
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/microRNA
Branch: RELEASE_3_7
Last Commit: 5e584a0
Last Changed Date: 2018-04-30 10:35:10 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: microRNA
Version: 1.38.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:microRNA.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings microRNA_1.38.0.tar.gz
StartedAt: 2018-10-16 02:00:58 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:01:57 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 58.1 seconds
RetCode: 0
Status:  OK 
CheckDir: microRNA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:microRNA.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings microRNA_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/microRNA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microRNA/DESCRIPTION’ ... OK
* this is package ‘microRNA’ version ‘1.38.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘microRNA’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data      5.4Mb
    extdata   2.0Mb
* checking package 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/microRNA.Rcheck/00check.log’
for details.



Installation output

microRNA.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL microRNA
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘microRNA’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c longest_common_substring.cpp -o longest_common_substring.o
longest_common_substring.cpp: In function ‘SEXPREC* longest_common_substring(SEXP)’:
longest_common_substring.cpp:55:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i == len[index] - 1) { // ignore null termination character
               ^
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o microRNA.so longest_common_substring.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/microRNA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (microRNA)

Tests output


Example timings

microRNA.Rcheck/microRNA-Ex.timings

nameusersystemelapsed
RNA2DNA000
get_selfhyb_subseq0.2000.0000.203
hsSeqs0.0040.0080.013
hsTargets0.3720.0120.385
matchSeeds2.5920.0442.639
mmSeqs0.0000.0000.002
mmTargets1.7200.0361.754
s3utr0.0040.0000.004
seedRegions0.0040.0000.003