Package: scmap

Version: 1.1.5

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings scmap_1.1.5.tar.gz

StartedAt: 2018-04-12 02:46:25 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:48:59 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 153.8 seconds

RetCode: 0

Status:  OK

CheckDir: scmap.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings scmap_1.1.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/scmap.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scmap’ version ‘1.1.5’
* package encoding: UTF-8
* 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 ‘scmap’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.2Mb
    libs   1.5Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Biobase’
  All declared Imports should be used.
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/scmap.Rcheck/00check.log’
for details.

* installing *source* package ‘scmap’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c scmap.cpp -o scmap.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o scmap.so RcppExports.o scmap.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/scmap.Rcheck/scmap/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
* DONE (scmap)

name	user	system	elapsed
getSankey	0.116	0.004	0.122
indexCell	3.692	0.080	3.774
indexCluster	2.116	0.040	2.159
scmapCell	1.292	0.024	1.314
scmapCell2Cluster	1.728	0.016	1.744
scmapCluster	1.396	0.016	1.416
selectFeatures	1.008	0.004	1.013
setFeatures	0.640	0.000	0.643