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CHECK report for scmap on celaya2

This page was generated on 2020-01-16 13:48:21 -0500 (Thu, 16 Jan 2020).

Package 1532/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scmap 1.9.0
Vladimir Kiselev
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/scmap
Branch: master
Last Commit: fc60ef0
Last Changed Date: 2019-10-29 13:42:21 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: scmap
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scmap_1.9.0.tar.gz
StartedAt: 2020-01-16 08:39:35 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 08:44:10 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 275.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: scmap.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scmap_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/scmap.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.9.0’
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'isSpike<-' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike<-' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike<-' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike<-' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike<-' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike<-' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike<-' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/scmap.Rcheck/00check.log’
for details.

Installation output

scmap.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scmap
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘scmap’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c scmap.cpp -o scmap.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o scmap.so RcppExports.o scmap.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-scmap/00new/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 from temporary location
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
** testing if installed package keeps a record of temporary installation path
* DONE (scmap)

Tests output

Example timings

scmap.Rcheck/scmap-Ex.timings

nameusersystemelapsed
getSankey0.0430.0110.054
indexCell3.7750.1563.936
indexCluster2.4000.1842.584
scmapCell1.2820.2111.493
scmapCell2Cluster2.0320.2472.280
scmapCluster2.5410.2092.751
selectFeatures1.1190.1621.281
setFeatures0.7990.1440.944