| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:40 -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 scGPS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scGPS.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 1807/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scGPS 1.15.0 (landing page) Quan Nguyen
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: scGPS |
| Version: 1.15.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scGPS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings scGPS_1.15.0.tar.gz |
| StartedAt: 2023-05-10 03:48:21 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 04:03:57 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 936.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scGPS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scGPS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings scGPS_1.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/scGPS.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 ‘scGPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scGPS’ version ‘1.15.0’
* 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 ‘scGPS’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
data 2.0Mb
libs 3.2Mb
* 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 ... NOTE
plot_reduced: no visible binding for global variable ‘..count..’
Undefined global functions or variables:
..count..
* 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 LazyData ... 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 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
find_markers 69.870 0.692 70.563
annotate_clusters 42.317 0.415 42.739
CORE_bagging 17.944 1.187 13.312
clustering_bagging 15.628 0.093 10.456
plot_reduced 14.781 0.120 14.901
tSNE 13.078 0.012 13.091
clustering 11.020 0.175 5.846
plot_optimal_CORE 11.082 0.048 5.989
PCA 10.362 0.116 10.480
CORE_subcluster 10.326 0.097 4.835
plot_CORE 10.005 0.065 4.865
CORE_clustering 9.871 0.129 4.807
rand_index 9.818 0.100 4.724
find_optimal_stability 9.807 0.055 4.728
find_stability 9.783 0.032 4.659
bootstrap_prediction 5.170 0.216 5.387
* 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 ...
‘vignette.Rmd’ using ‘UTF-8’... 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/scGPS.Rcheck/00check.log’
for details.
scGPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL scGPS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘scGPS’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -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/lib/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -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/lib/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c dist_mat_cpp.cpp -o dist_mat_cpp.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -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/lib/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c dist_parallel_cpp.cpp -o dist_parallel_cpp.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -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/lib/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c utils_rcpp.cpp -o utils_rcpp.o g++ -std=gnu++17 -shared -L/usr/local/lib -o scGPS.so RcppExports.o dist_mat_cpp.o dist_parallel_cpp.o utils_rcpp.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-scGPS/00new/scGPS/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (scGPS)
scGPS.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
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Type 'q()' to quit R.
> library(testthat)
> library(scGPS)
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
Loading required package: dynamicTreeCut
Loading required package: SingleCellExperiment
>
> test_check("scGPS")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
13.762 0.685 14.574
scGPS.Rcheck/scGPS-Ex.timings
| name | user | system | elapsed | |
| CORE_bagging | 17.944 | 1.187 | 13.312 | |
| CORE_clustering | 9.871 | 0.129 | 4.807 | |
| CORE_subcluster | 10.326 | 0.097 | 4.835 | |
| PCA | 10.362 | 0.116 | 10.480 | |
| PrinComp_cpp | 0.126 | 0.004 | 0.130 | |
| annotate_clusters | 42.317 | 0.415 | 42.739 | |
| bootstrap_parallel | 0.563 | 0.061 | 0.624 | |
| bootstrap_prediction | 5.170 | 0.216 | 5.387 | |
| calcDist | 0.420 | 0.276 | 0.696 | |
| calcDistArma | 0 | 0 | 0 | |
| clustering | 11.020 | 0.175 | 5.846 | |
| clustering_bagging | 15.628 | 0.093 | 10.456 | |
| distvec | 0 | 0 | 0 | |
| find_markers | 69.870 | 0.692 | 70.563 | |
| find_optimal_stability | 9.807 | 0.055 | 4.728 | |
| find_stability | 9.783 | 0.032 | 4.659 | |
| mean_cpp | 0.005 | 0.000 | 0.005 | |
| new_scGPS_object | 0.387 | 0.008 | 0.395 | |
| new_summarized_scGPS_object | 0.021 | 0.007 | 0.028 | |
| plot_CORE | 10.005 | 0.065 | 4.865 | |
| plot_optimal_CORE | 11.082 | 0.048 | 5.989 | |
| plot_reduced | 14.781 | 0.120 | 14.901 | |
| predicting | 1.863 | 0.072 | 1.936 | |
| rand_index | 9.818 | 0.100 | 4.724 | |
| rcpp_Eucl_distance_NotPar | 0.010 | 0.003 | 0.013 | |
| rcpp_parallel_distance | 0.123 | 0.000 | 0.123 | |
| reformat_LASSO | 4.661 | 0.040 | 4.701 | |
| sub_clustering | 0.163 | 0.005 | 0.145 | |
| subset_cpp | 0.131 | 0.000 | 0.132 | |
| summary_accuracy | 2.608 | 0.020 | 2.628 | |
| summary_deviance | 4.570 | 0.052 | 4.623 | |
| summary_prediction_lasso | 2.632 | 0.008 | 2.641 | |
| summary_prediction_lda | 2.597 | 0.016 | 2.612 | |
| tSNE | 13.078 | 0.012 | 13.091 | |
| top_var | 0.442 | 0.008 | 0.450 | |
| tp_cpp | 0.138 | 0.000 | 0.138 | |
| training | 0.879 | 0.016 | 0.895 | |
| var_cpp | 0.01 | 0.00 | 0.01 | |