Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-14 12:02 -0400 (Fri, 14 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4353 |
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 |
Package 1840/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scGPS 1.19.0 (landing page) Quan Nguyen
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: scGPS |
Version: 1.19.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scGPS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scGPS_1.19.0.tar.gz |
StartedAt: 2024-06-14 03:52:58 -0400 (Fri, 14 Jun 2024) |
EndedAt: 2024-06-14 04:02:29 -0400 (Fri, 14 Jun 2024) |
EllapsedTime: 570.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scGPS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scGPS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scGPS_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scGPS.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘scGPS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scGPS’ version ‘1.19.0’ * 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 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: data 2.1Mb libs 3.3Mb * 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 code 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 ... 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 40.522 0.580 41.103 annotate_clusters 32.208 0.308 32.518 CORE_bagging 9.188 0.910 7.490 clustering_bagging 8.408 0.102 5.978 plot_reduced 5.926 0.032 5.958 clustering 5.858 0.074 4.054 rand_index 5.534 0.027 3.369 plot_optimal_CORE 5.544 0.014 3.242 tSNE 5.176 0.000 5.176 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/scGPS.Rcheck/00check.log’ for details.
scGPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scGPS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘scGPS’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c dist_mat_cpp.cpp -o dist_mat_cpp.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c dist_parallel_cpp.cpp -o dist_parallel_cpp.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils_rcpp.cpp -o utils_rcpp.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -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-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/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 version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(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, 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: dynamicTreeCut Loading required package: SingleCellExperiment > > test_check("scGPS") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] > > proc.time() user system elapsed 10.035 0.801 10.831
scGPS.Rcheck/scGPS-Ex.timings
name | user | system | elapsed | |
CORE_bagging | 9.188 | 0.910 | 7.490 | |
CORE_clustering | 4.213 | 0.048 | 2.559 | |
CORE_subcluster | 4.292 | 0.015 | 2.507 | |
PCA | 3.586 | 0.048 | 3.635 | |
PrinComp_cpp | 0.127 | 0.012 | 0.140 | |
annotate_clusters | 32.208 | 0.308 | 32.518 | |
bootstrap_parallel | 0.380 | 0.008 | 0.389 | |
bootstrap_prediction | 2.496 | 0.016 | 2.513 | |
calcDist | 0.380 | 0.104 | 0.484 | |
calcDistArma | 0 | 0 | 0 | |
clustering | 5.858 | 0.074 | 4.054 | |
clustering_bagging | 8.408 | 0.102 | 5.978 | |
distvec | 0.001 | 0.000 | 0.001 | |
find_markers | 40.522 | 0.580 | 41.103 | |
find_optimal_stability | 4.676 | 0.066 | 2.661 | |
find_stability | 4.716 | 0.016 | 2.568 | |
mean_cpp | 0.003 | 0.000 | 0.002 | |
new_scGPS_object | 0.231 | 0.000 | 0.232 | |
new_summarized_scGPS_object | 0.020 | 0.001 | 0.020 | |
plot_CORE | 4.752 | 0.016 | 2.678 | |
plot_optimal_CORE | 5.544 | 0.014 | 3.242 | |
plot_reduced | 5.926 | 0.032 | 5.958 | |
predicting | 0.934 | 0.028 | 0.963 | |
rand_index | 5.534 | 0.027 | 3.369 | |
rcpp_Eucl_distance_NotPar | 0.013 | 0.000 | 0.013 | |
rcpp_parallel_distance | 0.137 | 0.004 | 0.142 | |
reformat_LASSO | 2.235 | 0.076 | 2.311 | |
sub_clustering | 0.112 | 0.001 | 0.071 | |
subset_cpp | 0.133 | 0.004 | 0.137 | |
summary_accuracy | 1.286 | 0.016 | 1.302 | |
summary_deviance | 2.311 | 0.020 | 2.331 | |
summary_prediction_lasso | 1.351 | 0.004 | 1.356 | |
summary_prediction_lda | 1.256 | 0.004 | 1.260 | |
tSNE | 5.176 | 0.000 | 5.176 | |
top_var | 0.223 | 0.000 | 0.223 | |
tp_cpp | 0.140 | 0.000 | 0.139 | |
training | 0.531 | 0.000 | 0.531 | |
var_cpp | 0.004 | 0.004 | 0.008 | |