Aaron Lun
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/SingleR |
| Branch: RELEASE_3_10 |
| Last Commit: 5803a1f |
| Last Changed Date: 2020-04-08 12:05:48 -0400 (Wed, 08 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:16:08 -0400 (Wed, 15 Apr 2020).
| Package 1606/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SingleR 1.0.6 Aaron Lun
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: SingleR |
| Version: 1.0.6 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SingleR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SingleR_1.0.6.tar.gz |
| StartedAt: 2020-04-15 06:51:01 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:00:25 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 564.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SingleR.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SingleR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SingleR_1.0.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/SingleR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SingleR/DESCRIPTION’ ... OK
* this is package ‘SingleR’ version ‘1.0.6’
* 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 ‘SingleR’ 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 ... WARNING
Codoc mismatches from documentation object 'plotScoreHeatmap':
plotScoreHeatmap
Code: function(results, cells.use = NULL, labels.use = NULL, clusters
= NULL, show.labels = TRUE, show.pruned = FALSE,
max.labels = 40, normalize = TRUE, cells.order = NULL,
order.by.clusters = FALSE, annotation_col = NULL,
show_colnames = FALSE, color = NULL, ...)
Docs: function(results, cells.use = NULL, labels.use = NULL, clusters
= NULL, show.labels = TRUE, show.pruned = FALSE,
max.labels = 40, normalize = TRUE, cells.order = NULL,
order.by.clusters = FALSE, annotation_col = NULL,
show_colnames = FALSE, ...)
Argument names in code not in docs:
color
Mismatches in argument names:
Position: 13 Code: color Docs: ...
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
DatabaseImmuneCellExpressionData 10.100 0.428 11.041
BlueprintEncodeData 8.840 0.276 9.832
plotScoreDistribution 7.540 0.012 7.698
HumanPrimaryCellAtlasData 6.308 0.152 6.869
MouseRNAseqData 5.728 0.096 6.089
ImmGenData 5.576 0.124 6.323
MonacoImmuneData 5.576 0.064 5.889
NovershternHematopoieticData 4.792 0.052 5.724
* 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-3.10-bioc/meat/SingleR.Rcheck/00check.log’
for details.
SingleR.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL SingleR
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I/usr/local/include -fpic -g -O2 -Wall -c fine_tune_de.cpp -o fine_tune_de.o
fine_tune_de.cpp: In constructor ‘de_markers::de_markers(Rcpp::List)’:
fine_tune_de.cpp:6:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i=0; i<marker_genes.size(); ++i) {
~^~~~~~~~~~~~~~~~~~~~
fine_tune_de.cpp:9:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j=0; j<internals.size(); ++j) {
~^~~~~~~~~~~~~~~~~
fine_tune_de.cpp: In function ‘Rcpp::List fine_tune_label_de(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::List)’:
fine_tune_de.cpp:38:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i=0; i<References.size(); ++i) {
~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_de.cpp:2:0:
fine_tuner.h: In instantiation of ‘tuned_stats fine_tuner::assign(int, beachmat::numeric_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = de_markers; tuned_stats = std::tuple<int, double, double>; beachmat::numeric_matrix = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > > >]’:
fine_tune_de.cpp:51:95: required from here
fine_tuner.h:42:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i=0; i<cur_scores.size(); ++i) {
~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I/usr/local/include -fpic -g -O2 -Wall -c fine_tune_sd.cpp -o fine_tune_sd.o
fine_tune_sd.cpp: In function ‘Rcpp::List fine_tune_label_sd(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::NumericMatrix, double)’:
fine_tune_sd.cpp:46:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i=0; i<References.size(); ++i) {
~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_sd.cpp:2:0:
fine_tuner.h: In instantiation of ‘tuned_stats fine_tuner::assign(int, beachmat::numeric_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = sd_markers; tuned_stats = std::tuple<int, double, double>; beachmat::numeric_matrix = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > > >]’:
fine_tune_sd.cpp:59:95: required from here
fine_tuner.h:42:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i=0; i<cur_scores.size(); ++i) {
~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o SingleR.so RcppExports.o fine_tune_de.o fine_tune_sd.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-SingleR/00new/SingleR/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 (SingleR)
SingleR.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(SingleR)
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
> test_check("SingleR")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 362 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
217.580 4.988 302.953
SingleR.Rcheck/SingleR-Ex.timings
| name | user | system | elapsed | |
| BlueprintEncodeData | 8.840 | 0.276 | 9.832 | |
| DatabaseImmuneCellExpressionData | 10.100 | 0.428 | 11.041 | |
| HumanPrimaryCellAtlasData | 6.308 | 0.152 | 6.869 | |
| ImmGenData | 5.576 | 0.124 | 6.323 | |
| MonacoImmuneData | 5.576 | 0.064 | 5.889 | |
| MouseRNAseqData | 5.728 | 0.096 | 6.089 | |
| NovershternHematopoieticData | 4.792 | 0.052 | 5.724 | |
| SingleR | 1.444 | 0.012 | 1.463 | |
| aggregateReference | 1.212 | 0.028 | 1.240 | |
| classifySingleR | 0.316 | 0.008 | 0.326 | |
| combineResults | 1.144 | 0.000 | 1.142 | |
| getDeltaFromMedian | 0.684 | 0.000 | 0.705 | |
| matchReferences | 0.892 | 0.004 | 0.897 | |
| plotScoreDistribution | 7.540 | 0.012 | 7.698 | |
| plotScoreHeatmap | 1.768 | 0.008 | 1.779 | |
| pruneScores | 0.696 | 0.000 | 0.698 | |
| trainSingleR | 1.580 | 0.004 | 1.619 | |