| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:41 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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To the developers/maintainers of the scran package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scran.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 1828/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scran 1.29.0 (landing page) Aaron Lun
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: scran |
| Version: 1.29.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings scran_1.29.0.tar.gz |
| StartedAt: 2023-06-06 06:29:32 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 06:50:50 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 1277.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scran.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings scran_1.29.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/scran.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘scran/DESCRIPTION’ ... OK
* this is package ‘scran’ version ‘1.29.0’
* 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 ‘scran’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 11.8Mb
sub-directories of 1Mb or more:
libs 10.8Mb
* 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 loading without being on the library search path ... 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 ... WARNING
Found the following significant warnings:
Warning: 'combinePValues' is deprecated.
Warning: 'combinePValues' is deprecated.
Warning: 'combinePValues' is deprecated.
Warning: 'combinePValues' is deprecated.
Warning: 'correlateNull' is deprecated.
Warning: 'correlateNull' is deprecated.
Warning: 'correlateNull' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cyclone 30.407 0.252 30.707
buildSNNGraph 11.773 0.144 11.934
decideTestsPerLabel 7.146 0.080 7.243
quickSubCluster 6.238 0.024 6.276
pseudoBulkSpecific 5.060 0.024 5.092
* 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 ...
‘scran.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/scran.Rcheck/00check.log’
for details.
scran.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL scran ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘scran’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -c choose_effect_size.cpp -o choose_effect_size.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -c combine_rho.cpp -o combine_rho.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -c compute_blocked_stats.cpp -o compute_blocked_stats.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -c compute_residual_stats.cpp -o compute_residual_stats.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -c compute_rho_null.cpp -o compute_rho_null.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -c cyclone_scores.cpp -o cyclone_scores.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -c overlap_exprs.cpp -o overlap_exprs.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -c rand_custom.cpp -o rand_custom.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o scran.so RcppExports.o choose_effect_size.o combine_rho.o compute_blocked_stats.o compute_residual_stats.o compute_rho_null.o cyclone_scores.o overlap_exprs.o rand_custom.o -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-scran/00new/scran/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 (scran)
scran.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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(scran)
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 object is masked from 'package:utils':
findMatches
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
Loading required package: scuttle
> test_check("scran")
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
using C++ compiler: ‘g++ (GCC) 10.3.1’
[ FAIL 0 | WARN 5069 | SKIP 1 | PASS 4479 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• monocle is a little broken because of clusterApply (1)
[ FAIL 0 | WARN 5069 | SKIP 1 | PASS 4479 ]
>
> proc.time()
user system elapsed
557.498 14.535 656.715
scran.Rcheck/scran-Ex.timings
| name | user | system | elapsed | |
| DM | 0.807 | 0.036 | 0.844 | |
| buildSNNGraph | 11.773 | 0.144 | 11.934 | |
| clusterCells | 1.868 | 0.016 | 1.888 | |
| combineBlocks | 1.450 | 0.012 | 1.465 | |
| combineMarkers | 2.025 | 0.020 | 2.049 | |
| combinePValues | 0.035 | 0.000 | 0.035 | |
| combineVar | 2.271 | 0.064 | 2.338 | |
| computeMinRank | 0.003 | 0.000 | 0.003 | |
| convertTo | 1.681 | 0.019 | 1.705 | |
| correlateGenes | 1.147 | 0.023 | 1.174 | |
| correlateNull | 0.251 | 0.000 | 0.252 | |
| correlatePairs | 1.171 | 0.012 | 1.185 | |
| cyclone | 30.407 | 0.252 | 30.707 | |
| decideTestsPerLabel | 7.146 | 0.080 | 7.243 | |
| defunct | 0.001 | 0.000 | 0.001 | |
| denoisePCA | 2.180 | 0.004 | 2.187 | |
| findMarkers | 2.861 | 0.016 | 2.883 | |
| fitTrendCV2 | 0.761 | 0.004 | 0.767 | |
| fitTrendPoisson | 0.205 | 0.000 | 0.205 | |
| fitTrendVar | 0.886 | 0.000 | 0.888 | |
| fixedPCA | 1.469 | 0.004 | 1.475 | |
| getClusteredPCs | 4.127 | 0.004 | 4.138 | |
| getMarkerEffects | 1.282 | 0.023 | 1.308 | |
| getTopHVGs | 1.109 | 0.004 | 1.115 | |
| getTopMarkers | 1.308 | 0.000 | 1.310 | |
| logBH | 0.001 | 0.000 | 0.001 | |
| modelGeneCV2 | 1.222 | 0.004 | 1.228 | |
| modelGeneCV2WithSpikes | 2.084 | 0.052 | 2.140 | |
| modelGeneVar | 1.452 | 0.004 | 1.459 | |
| modelGeneVarByPoisson | 1.229 | 0.012 | 1.243 | |
| modelGeneVarWithSpikes | 2.239 | 0.008 | 2.251 | |
| multiMarkerStats | 2.082 | 0.004 | 2.091 | |
| pairwiseBinom | 1.077 | 0.000 | 1.080 | |
| pairwiseTTests | 1.187 | 0.036 | 1.226 | |
| pairwiseWilcox | 1.021 | 0.019 | 1.043 | |
| pseudoBulkDGE | 3.414 | 0.024 | 3.444 | |
| pseudoBulkSpecific | 5.060 | 0.024 | 5.092 | |
| quickCluster | 3.644 | 0.000 | 3.652 | |
| quickSubCluster | 6.238 | 0.024 | 6.276 | |
| rhoToPValue | 0.001 | 0.000 | 0.001 | |
| sandbag | 0.993 | 0.004 | 1.001 | |
| scaledColRanks | 2.490 | 0.000 | 2.494 | |
| scoreMarkers | 1.419 | 0.012 | 1.434 | |
| summaryMarkerStats | 1.155 | 0.012 | 1.170 | |
| testLinearModel | 0.076 | 0.000 | 0.076 | |