Davis McCarthy
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/scater |
| Branch: RELEASE_3_7 |
| Last Commit: d560a9a |
| Last Changed Date: 2018-08-13 06:13:02 -0400 (Mon, 13 Aug 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:56:00 -0400 (Wed, 17 Oct 2018).
| Package 1320/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scater 1.8.4 Davis McCarthy
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: scater |
| Version: 1.8.4 |
| 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_1.8.4.tar.gz |
| StartedAt: 2018-10-16 23:55:25 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-17 00:01:12 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 346.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scater.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running 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_1.8.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/scater.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.4’
* 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 9.4Mb
sub-directories of 1Mb or more:
extdata 2.9Mb
libs 4.8Mb
* 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 ‘_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: 'read10xResults' is deprecated.
Warning: 'downsampleCounts' is deprecated.
Warning: 'normalizeExprs' is deprecated.
Warning: 'normalizeExprs' is deprecated.
Warning: 'normalizeExprs' is deprecated.
Warning: 'normalizeExprs' is deprecated.
Warning: 'normalizeExprs' is deprecated.
Warning: 'normalizeExprs' is deprecated.
Warning: 'read10xResults' 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
plot_reddim 6.906 0.105 7.105
plotRLE 5.166 0.263 5.472
* 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-3.7-bioc/meat/scater.Rcheck/00check.log’
for details.
scater.Rcheck/00install.out
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###
### Running command:
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### /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
In file included from calc_exprs.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
int iterateAttrs() { return 0; }
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
^
In file included from calc_exprs.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
void renameAttr() {}
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
virtual void renameAttr(const char* oldname, const char* newname) const;
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
^
2 warnings generated.
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_top_features.cpp -o calc_top_features.o
In file included from calc_top_features.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
int iterateAttrs() { return 0; }
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
^
In file included from calc_top_features.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
void renameAttr() {}
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
virtual void renameAttr(const char* oldname, const char* newname) const;
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
^
2 warnings generated.
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
In file included from init.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
int iterateAttrs() { return 0; }
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
^
In file included from init.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
void renameAttr() {}
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
virtual void renameAttr(const char* oldname, const char* newname) const;
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
^
2 warnings generated.
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 matrix_stats.cpp -o matrix_stats.o
In file included from matrix_stats.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
int iterateAttrs() { return 0; }
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
^
In file included from matrix_stats.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
void renameAttr() {}
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
virtual void renameAttr(const char* oldname, const char* newname) const;
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
^
2 warnings generated.
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 calc_top_features.o init.o matrix_stats.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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ggplot2
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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: 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
Attaching package: 'scater'
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:stats':
filter
>
> test_check("scater")
Collapsing expression to 500 features.Collapsing expression to 500 features.Collapsing expression to 500 features.Collapsing expression to 500 features.Collapsing expression to 500 features.Kallisto log not provided - assuming all runs successfulCollapsing expression to 500 features.Kallisto log not provided - assuming all runs successful══ testthat results ═══════════════════════════════════════════════════════════
OK: 1014 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
85.275 2.184 88.244
scater.Rcheck/scater-Ex.timings
| name | user | system | elapsed | |
| accessors | 0.692 | 0.066 | 0.763 | |
| areSizeFactorsCentred | 0.089 | 0.002 | 0.093 | |
| arrange | 0.111 | 0.005 | 0.119 | |
| bootstraps | 0.076 | 0.004 | 0.080 | |
| calcAverage | 0.082 | 0.005 | 0.087 | |
| calcIsExprs | 0.090 | 0.004 | 0.096 | |
| calculateCPM | 0.121 | 0.010 | 0.133 | |
| calculateFPKM | 0.115 | 0.007 | 0.124 | |
| calculateQCMetrics | 0.979 | 0.047 | 1.037 | |
| calculateTPM | 0.173 | 0.010 | 0.184 | |
| centreSizeFactors | 0.078 | 0.004 | 0.083 | |
| downsampleCounts | 0.242 | 0.013 | 0.262 | |
| filter | 0.068 | 0.003 | 0.072 | |
| findImportantPCs | 2.033 | 0.039 | 2.088 | |
| getBMFeatureAnnos | 0.001 | 0.000 | 0.002 | |
| isOutlier | 0.540 | 0.022 | 0.562 | |
| kallisto-wrapper | 0.003 | 0.000 | 0.002 | |
| librarySizeFactors | 0.009 | 0.001 | 0.012 | |
| multiplot | 2.231 | 0.026 | 2.276 | |
| mutate | 0.059 | 0.004 | 0.066 | |
| nexprs | 0.112 | 0.004 | 0.118 | |
| normalize | 0.890 | 0.034 | 0.929 | |
| normalizeExprs | 0.291 | 0.022 | 0.315 | |
| plotColData | 2.122 | 0.041 | 2.186 | |
| plotExplanatoryVariables | 1.457 | 0.050 | 1.529 | |
| plotExpression | 4.241 | 0.045 | 4.332 | |
| plotExprsFreqVsMean | 1.777 | 0.030 | 1.830 | |
| plotExprsVsTxLength | 2.961 | 0.055 | 3.044 | |
| plotHeatmap | 0.763 | 0.027 | 0.799 | |
| plotHighestExprs | 2.362 | 0.017 | 2.403 | |
| plotPlatePosition | 1.742 | 0.011 | 1.764 | |
| plotQC | 3.092 | 0.053 | 3.171 | |
| plotRLE | 5.166 | 0.263 | 5.472 | |
| plotReducedDim | 4.903 | 0.025 | 4.970 | |
| plotRowData | 1.977 | 0.015 | 2.014 | |
| plotScater | 3.906 | 0.129 | 4.079 | |
| plot_reddim | 6.906 | 0.105 | 7.105 | |
| read10xResults | 0.179 | 0.007 | 0.187 | |
| readTxResults | 0.002 | 0.000 | 0.002 | |
| rename | 0.075 | 0.005 | 0.080 | |
| runDiffusionMap | 0.230 | 0.007 | 0.239 | |
| runMDS | 0.150 | 0.008 | 0.162 | |
| runPCA | 0.144 | 0.010 | 0.156 | |
| runTSNE | 0.476 | 0.010 | 0.493 | |
| salmon-wrapper | 0.003 | 0.000 | 0.003 | |
| scater_gui | 0.768 | 0.012 | 0.789 | |
| summariseExprsAcrossFeatures | 1.132 | 0.079 | 1.234 | |
| toSingleCellExperiment | 0.001 | 0.000 | 0.002 | |
| uniquifyFeatureNames | 0.002 | 0.001 | 0.002 | |