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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-14 12:20:11 -0500 (Tue, 14 Jan 2020).
| Package 1523/1813 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scfind 1.9.0 Vladimir Kiselev
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| 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 | |
| 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 |
##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################
* 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.
scfind.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL scfind
###
##############################################################################
##############################################################################
* 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)
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
scfind.Rcheck/scfind-Ex.timings
| name | user | system | elapsed | |
| buildCellIndex | 24.467 | 0.263 | 25.350 | |
| buildCellTypeIndex | 2.853 | 0.047 | 3.063 | |
| findCell | 21.996 | 0.020 | 22.566 | |
| findCellType | 2.267 | 0.028 | 2.374 | |