Davis McCarthy
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/scater |
| Branch: RELEASE_3_8 |
| Last Commit: 2e6694a |
| Last Changed Date: 2019-01-04 13:48:22 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:59:19 -0400 (Tue, 16 Apr 2019).
| Package 1391/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scater 1.10.1 Davis McCarthy
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: scater |
| Version: 1.10.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scater.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scater_1.10.1.tar.gz |
| StartedAt: 2019-04-16 02:36:58 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:45:00 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 482.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scater.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scater.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scater_1.10.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/scater.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scater’ version ‘1.10.1’
* 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 ‘scater’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
libs 4.9Mb
* 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/scater/libs/scater.so’:
Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_exit’, possibly from ‘exit’ (C)
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘_rand_r’, possibly from ‘rand_r’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: 'calcIsExprs' is deprecated.
Warning: 'plotQC' is deprecated.
Warning: 'add_ticks' is deprecated.
Warning: 'add_ticks' is deprecated.
Warning: 'add_ticks' is deprecated.
Warning: 'add_ticks' is deprecated.
Warning: 'add_ticks' is deprecated.
Warning: 'add_ticks' is deprecated.
Warning: 'add_ticks' is deprecated.
Warning: 'add_ticks' is deprecated.
Warning: 'add_ticks' is deprecated.
Warning: 'add_ticks' is deprecated.
Warning: 'add_ticks' is deprecated.
Warning: 'readTxResults' is deprecated.
Warning: 'summariseExprsAcrossFeatures' is deprecated.
Warning: 'summariseExprsAcrossFeatures' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
readTxResults 12.237 0.553 12.964
plot_reddim 6.026 0.070 6.153
* 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/scater.Rcheck/00check.log’
for details.
scater.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scater ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘scater’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I/usr/local/include -fPIC -Wall -g -O2 -c calc_exprs.cpp -o calc_exprs.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I/usr/local/include -fPIC -Wall -g -O2 -c combined_qc.cpp -o combined_qc.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I/usr/local/include -fPIC -Wall -g -O2 -c num_exprs.cpp -o num_exprs.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I/usr/local/include -fPIC -Wall -g -O2 -c sum_counts.cpp -o sum_counts.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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 scater.so calc_exprs.o combined_qc.o init.o num_exprs.o sum_counts.o utils.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/lib/libbeachmat.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libsz.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/scater/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘mutate’ in package ‘scater’ Creating a new generic function for ‘filter’ in package ‘scater’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (scater)
scater.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(scater)
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, lengths, 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
Loading required package: ggplot2
Attaching package: 'scater'
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:stats':
filter
>
> test_check("scater")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 1210 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
99.258 4.498 230.780
scater.Rcheck/scater-Ex.timings
| name | user | system | elapsed | |
| accessors | 1.306 | 0.021 | 1.343 | |
| arrange | 0.094 | 0.006 | 0.102 | |
| bootstraps | 0.079 | 0.005 | 0.085 | |
| calcIsExprs | 0.085 | 0.004 | 0.090 | |
| calculateAverage | 0.101 | 0.014 | 0.117 | |
| calculateCPM | 0.107 | 0.020 | 0.127 | |
| calculateFPKM | 0.082 | 0.017 | 0.099 | |
| calculateQCMetrics | 0.454 | 0.008 | 0.467 | |
| calculateTPM | 0.131 | 0.005 | 0.135 | |
| centreSizeFactors | 0.072 | 0.007 | 0.080 | |
| filter | 0.117 | 0.020 | 0.138 | |
| getBMFeatureAnnos | 0.001 | 0.000 | 0.000 | |
| getExplanatoryPCs | 0.253 | 0.009 | 0.267 | |
| getVarianceExplained | 0.162 | 0.013 | 0.176 | |
| isOutlier | 0.302 | 0.010 | 0.313 | |
| librarySizeFactors | 0.012 | 0.002 | 0.015 | |
| multiplot | 2.060 | 0.024 | 2.104 | |
| mutate | 0.058 | 0.004 | 0.062 | |
| nexprs | 0.085 | 0.005 | 0.093 | |
| normalize | 0.076 | 0.003 | 0.078 | |
| normalizeCounts | 0.010 | 0.004 | 0.014 | |
| plotColData | 2.019 | 0.020 | 2.055 | |
| plotExplanatoryPCs | 0.681 | 0.007 | 0.693 | |
| plotExplanatoryVariables | 0.542 | 0.019 | 0.569 | |
| plotExpression | 3.795 | 0.046 | 3.871 | |
| plotExprsFreqVsMean | 1.421 | 0.024 | 1.460 | |
| plotExprsVsTxLength | 3.453 | 0.074 | 3.563 | |
| plotHeatmap | 0.396 | 0.011 | 0.409 | |
| plotHighestExprs | 1.406 | 0.012 | 1.427 | |
| plotPlatePosition | 1.471 | 0.007 | 1.496 | |
| plotQC | 0.604 | 0.005 | 0.614 | |
| plotRLE | 2.435 | 0.116 | 2.571 | |
| plotReducedDim | 4.114 | 0.030 | 4.171 | |
| plotRowData | 1.305 | 0.015 | 1.335 | |
| plotScater | 3.085 | 0.132 | 3.241 | |
| plot_reddim | 6.026 | 0.070 | 6.153 | |
| readSparseCounts | 0.027 | 0.000 | 0.028 | |
| readTxResults | 12.237 | 0.553 | 12.964 | |
| rename | 0.081 | 0.007 | 0.089 | |
| runDiffusionMap | 0.203 | 0.024 | 0.227 | |
| runMDS | 0.156 | 0.011 | 0.170 | |
| runPCA | 0.109 | 0.005 | 0.114 | |
| runTSNE | 0.215 | 0.006 | 0.224 | |
| runUMAP | 1.542 | 0.412 | 1.977 | |
| sumCountsAcrossFeatures | 0.067 | 0.003 | 0.070 | |
| summariseExprsAcrossFeatures | 1.158 | 0.085 | 1.257 | |
| toSingleCellExperiment | 0.002 | 0.000 | 0.001 | |
| uniquifyFeatureNames | 0.002 | 0.000 | 0.002 | |