| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:41 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the scuttle package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scuttle.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1837/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scuttle 1.11.0 (landing page) Aaron Lun
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: scuttle |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scuttle.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings scuttle_1.11.0.tar.gz |
| StartedAt: 2023-05-10 04:17:48 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 04:30:34 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 766.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scuttle.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scuttle.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings scuttle_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/scuttle.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘scuttle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scuttle’ version ‘1.11.0’
* 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 ‘scuttle’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 8.9Mb
sub-directories of 1Mb or more:
libs 8.4Mb
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
computePooledFactors 10.114 0.268 10.382
downsampleBatches 5.013 0.224 5.237
* 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 ...
‘misc.Rmd’... OK
‘norm.Rmd’... OK
‘qc.Rmd’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/scuttle.Rcheck/00check.log’
for details.
scuttle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL scuttle ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘scuttle’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I/usr/local/include -fPIC -g -O2 -c cumulative_prop.cpp -o cumulative_prop.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I/usr/local/include -fPIC -g -O2 -c downsample_counts.cpp -o downsample_counts.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I/usr/local/include -fPIC -g -O2 -c fit_linear_model.cpp -o fit_linear_model.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I/usr/local/include -fPIC -g -O2 -c pool_size_factors.cpp -o pool_size_factors.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I/usr/local/include -fPIC -g -O2 -c sparse_summarize.cpp -o sparse_summarize.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I/usr/local/include -fPIC -g -O2 -c sum_counts.cpp -o sum_counts.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I/usr/local/include -fPIC -g -O2 -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/usr/local/lib -o scuttle.so RcppExports.o cumulative_prop.o downsample_counts.o fit_linear_model.o pool_size_factors.o sparse_summarize.o sum_counts.o utils.o -llapack -L/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/lib -lRblas -lgfortran -lm installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-scuttle/00new/scuttle/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 (scuttle)
scuttle.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(scuttle)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, 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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
> test_check("scuttle")
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: S4Arrays
Attaching package: 'S4Arrays'
The following object is masked from 'package:base':
rowsum
Loading required package: SparseArray
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, scale, sweep
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 1699 ]
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 1699 ]
>
> proc.time()
user system elapsed
159.960 9.419 197.691
scuttle.Rcheck/scuttle-Ex.timings
| name | user | system | elapsed | |
| addPerCellQCMetrics | 1.229 | 0.052 | 1.281 | |
| aggregateAcrossCells | 2.475 | 0.112 | 2.587 | |
| aggregateAcrossFeatures | 0.621 | 0.056 | 0.677 | |
| calculateAverage | 0.591 | 0.016 | 0.607 | |
| calculateCPM | 1.269 | 0.012 | 1.280 | |
| calculateFPKM | 0.515 | 0.004 | 0.519 | |
| calculateTPM | 0.500 | 0.008 | 0.508 | |
| cleanSizeFactors | 0.023 | 0.000 | 0.024 | |
| computePooledFactors | 10.114 | 0.268 | 10.382 | |
| computeSpikeFactors | 0.644 | 0.056 | 0.700 | |
| correctGroupSummary | 0.062 | 0.016 | 0.077 | |
| downsampleBatches | 5.013 | 0.224 | 5.237 | |
| downsampleMatrix | 3.019 | 0.060 | 3.079 | |
| fitLinearModel | 0.092 | 0.012 | 0.104 | |
| geometricSizeFactors | 0.518 | 0.044 | 0.562 | |
| isOutlier | 0.941 | 0.068 | 1.009 | |
| librarySizeFactors | 0.506 | 0.024 | 0.529 | |
| logNormCounts | 1.764 | 0.028 | 1.792 | |
| makePerCellDF | 0.958 | 0.028 | 0.986 | |
| makePerFeatureDF | 0.775 | 0.024 | 0.799 | |
| medianSizeFactors | 0.506 | 0.008 | 0.514 | |
| mockSCE | 0.583 | 0.016 | 0.598 | |
| normalizeCounts | 1.562 | 0.020 | 1.583 | |
| numDetectedAcrossCells | 0.584 | 0.008 | 0.591 | |
| numDetectedAcrossFeatures | 0.499 | 0.028 | 0.526 | |
| perCellQCFilters | 0.942 | 0.044 | 0.987 | |
| perCellQCMetrics | 1.836 | 0.008 | 1.845 | |
| perFeatureQCMetrics | 0.640 | 0.011 | 0.651 | |
| quickPerCellQC | 1.486 | 0.008 | 1.493 | |
| readSparseCounts | 0.008 | 0.000 | 0.008 | |
| sumCountsAcrossCells | 0.572 | 0.020 | 0.592 | |
| sumCountsAcrossFeatures | 0.503 | 0.019 | 0.522 | |
| summarizeAssayByGroup | 0.639 | 0.032 | 0.671 | |
| uniquifyFeatureNames | 0 | 0 | 0 | |