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CHECK report for scmap on malbec1

This page was generated on 2019-04-16 11:52:52 -0400 (Tue, 16 Apr 2019).

Package 1398/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scmap 1.4.1
Vladimir Kiselev
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/scmap
Branch: RELEASE_3_8
Last Commit: 1e83b1a
Last Changed Date: 2019-01-04 13:48:51 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scmap
Version: 1.4.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:scmap.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings scmap_1.4.1.tar.gz
StartedAt: 2019-04-16 02:54:28 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:57:03 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 154.7 seconds
RetCode: 0
Status:  OK 
CheckDir: scmap.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:scmap.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings scmap_1.4.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/scmap.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 ‘scmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scmap’ version ‘1.4.1’
* 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 ... 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 ... 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 ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/scmap.Rcheck/00check.log’
for details.



Installation output

scmap.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL scmap
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘scmap’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:514:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c scmap.cpp -o scmap.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from scmap.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:514:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o scmap.so RcppExports.o scmap.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/scmap/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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)

Tests output


Example timings

scmap.Rcheck/scmap-Ex.timings

nameusersystemelapsed
getSankey0.0360.0040.038
indexCell3.2680.0923.364
indexCluster2.0200.0162.039
scmapCell1.8000.0361.841
scmapCell2Cluster1.3600.0401.402
scmapCluster1.1160.0081.125
selectFeatures1.1480.0441.193
setFeatures0.5320.0280.561