Package: microRNA

Version: 1.41.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:microRNA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings microRNA_1.41.0.tar.gz

StartedAt: 2019-04-09 01:59:25 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:01:08 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 102.2 seconds

RetCode: 0

Status:  OK

CheckDir: microRNA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:microRNA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings microRNA_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/microRNA.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.41.0’
* 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-3.9-bioc/meat/microRNA.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL microRNA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘microRNA’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o microRNA.so longest_common_substring.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-microRNA/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (microRNA)

name	user	system	elapsed
RNA2DNA	0.001	0.000	0.000
get_selfhyb_subseq	0.040	0.001	0.041
hsSeqs	0.018	0.000	0.018
hsTargets	0.517	0.019	0.538
matchSeeds	4.278	0.096	4.485
mmSeqs	0.003	0.000	0.002
mmTargets	2.429	0.071	2.564
s3utr	0.006	0.000	0.006
seedRegions	0.004	0.000	0.004