Aaron Lun
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/batchelor |
| Branch: master |
| Last Commit: 4ff6842 |
| Last Changed Date: 2019-03-27 00:58:14 -0400 (Wed, 27 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:22:06 -0400 (Tue, 09 Apr 2019).
| Package 107/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| batchelor 0.99.7 Aaron Lun
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: batchelor |
| Version: 0.99.7 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:batchelor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings batchelor_0.99.7.tar.gz |
| StartedAt: 2019-04-09 00:02:38 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 00:08:22 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 344.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: batchelor.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:batchelor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings batchelor_0.99.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/batchelor.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘batchelor/DESCRIPTION’ ... OK * this is package ‘batchelor’ version ‘0.99.7’ * 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 ‘batchelor’ 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 line endings in C/C++/Fortran sources/headers ... 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 ‘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 NOTE See ‘/Users/biocbuild/bbs-3.9-bioc/meat/batchelor.Rcheck/00check.log’ for details.
batchelor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL batchelor ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘batchelor’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include -fPIC -Wall -g -O2 -c adjust_shift_variance.cpp -o adjust_shift_variance.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cosine_norm.cpp -o cosine_norm.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include -fPIC -Wall -g -O2 -c find_mutual_nns.cpp -o find_mutual_nns.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include -fPIC -Wall -g -O2 -c smooth_gaussian_kernel.cpp -o smooth_gaussian_kernel.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include -fPIC -Wall -g -O2 -c unlog_exprs.cpp -o unlog_exprs.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.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 batchelor.so adjust_shift_variance.o cosine_norm.o find_mutual_nns.o init.o smooth_gaussian_kernel.o unlog_exprs.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-batchelor/00new/batchelor/libs ** R ** 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 (batchelor)
batchelor.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(batchelor)
Loading required package: 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, colMeans, colSums, 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, rowMeans, rowSums,
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
> test_check("batchelor")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 1251 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
112.683 13.905 120.762
batchelor.Rcheck/batchelor-Ex.timings
| name | user | system | elapsed | |
| BatchelorParam | 0.122 | 0.027 | 0.150 | |
| batchCorrect | 1.046 | 0.153 | 1.204 | |
| checkInputs | 0.002 | 0.000 | 0.002 | |
| cosineNorm | 0.005 | 0.001 | 0.005 | |
| divideIntoBatches | 0.004 | 0.000 | 0.003 | |
| fastMNN | 0.510 | 0.011 | 0.522 | |
| findMutualNN | 0.028 | 0.001 | 0.028 | |
| mnnCorrect | 0.087 | 0.005 | 0.092 | |
| multiBatchNorm | 0.498 | 0.003 | 0.506 | |
| multiBatchPCA | 0.141 | 0.002 | 0.144 | |
| rescaleBatches | 0.065 | 0.001 | 0.066 | |