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CHECK report for scfind on malbec2

This page was generated on 2020-01-14 12:20:11 -0500 (Tue, 14 Jan 2020).

Package 1523/1813HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scfind 1.9.0
Vladimir Kiselev
Snapshot Date: 2020-01-13 16:45:51 -0500 (Mon, 13 Jan 2020)
URL: https://git.bioconductor.org/packages/scfind
Branch: master
Last Commit: 3b71b64
Last Changed Date: 2019-10-29 13:42:28 -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  NA 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: scfind
Version: 1.9.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:scfind.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings scfind_1.9.0.tar.gz
StartedAt: 2020-01-14 06:38:36 -0500 (Tue, 14 Jan 2020)
EndedAt: 2020-01-14 06:43:17 -0500 (Tue, 14 Jan 2020)
EllapsedTime: 280.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: scfind.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:scfind.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings scfind_1.9.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/scfind.Rcheck’
* using R Under development (unstable) (2019-12-14 r77569)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scfind/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scfind’ 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 ‘scfind’ 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 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.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
buildCellIndex 24.467  0.263  25.350
findCell       21.996  0.020  22.566
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/scfind.Rcheck/00check.log’
for details.



Installation output

scfind.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL scfind
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘scfind’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c eliasFano.cpp -o eliasFano.o
eliasFano.cpp: In function ‘std::vector<bool> int2bin(int)’:
eliasFano.cpp:8:9: warning: unused variable ‘rem’ [-Wunused-variable]
     int rem;
         ^~~
eliasFano.cpp: In function ‘Rcpp::NumericVector eliasFanoDecoding(Rcpp::LogicalVector, Rcpp::LogicalVector, int)’:
eliasFano.cpp:83:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int k = 0; k < h.size(); k++) {
                             ~~^~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o scfind.so RcppExports.o eliasFano.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-scfind/00new/scfind/libs
** R
** data
*** moving datasets to lazyload DB
** 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 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 (scfind)

Tests output

scfind.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-12-14 r77569) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(SingleCellExperiment)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

> library(scfind)
> 
> test_check("scfind")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 48 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 51.204   0.699  52.457 

Example timings

scfind.Rcheck/scfind-Ex.timings

nameusersystemelapsed
buildCellIndex24.467 0.26325.350
buildCellTypeIndex2.8530.0473.063
findCell21.996 0.02022.566
findCellType2.2670.0282.374