Package: dexus

Version: 1.22.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:dexus.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings dexus_1.22.1.tar.gz

StartedAt: 2019-04-15 23:29:02 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:29:44 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 42.5 seconds

RetCode: 0

Status:  OK

CheckDir: dexus.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:dexus.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings dexus_1.22.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/dexus.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dexus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dexus’ version ‘1.22.1’
* 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 ‘dexus’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/dexus.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL dexus
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘dexus’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c dexus.cpp -o dexus.o
dexus.cpp: In function ‘SEXPREC* dexus_impl(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP)’:
dexus.cpp:193:15: warning: unused variable ‘DEFAULT_R’ [-Wunused-variable]
  const double DEFAULT_R = 20; // R value used when re-setting clusters
               ^
dexus.cpp: In function ‘SEXPREC* dexss_impl(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP)’:
dexus.cpp:575:15: warning: unused variable ‘DEFAULT_R’ [-Wunused-variable]
  const double DEFAULT_R = 20; // R value used when re-setting clusters
               ^
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o dexus.so dexus.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/dexus/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dexus)

name	user	system	elapsed
DEXUSResult-class	0.000	0.004	0.002
DEXUSResult-subset	1.420	0.088	1.513
INI	1.528	0.012	1.541
INIThreshold-set	0.772	0.008	0.778
accessors	0.656	0.020	0.678
dexss	1.556	0.020	1.599
dexus	1.024	0.004	1.036
dexus.parallel	0.948	0.028	0.980
getSizeNB	0	0	0
normalizeData	0.976	0.020	1.000
plot	1.392	0.012	1.411
sort	1.484	0.000	1.484