Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 1839/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scGPS 1.14.1 (landing page) Quan Nguyen
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the scGPS package: - 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: 1.14.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scGPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scGPS_1.14.1.tar.gz |
StartedAt: 2023-10-18 22:22:24 -0400 (Wed, 18 Oct 2023) |
EndedAt: 2023-10-18 22:36:19 -0400 (Wed, 18 Oct 2023) |
EllapsedTime: 835.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scGPS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scGPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scGPS_1.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/scGPS.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scGPS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scGPS’ version ‘1.14.1’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... 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 85.908 1.016 152.766 annotate_clusters 39.145 1.515 72.492 CORE_bagging 10.400 0.174 17.045 clustering_bagging 8.967 0.118 14.515 plot_reduced 6.357 0.133 11.084 tSNE 5.585 0.106 10.142 plot_optimal_CORE 5.550 0.092 8.106 find_optimal_stability 4.780 0.090 6.821 plot_CORE 4.741 0.070 6.589 CORE_clustering 4.732 0.064 6.613 clustering 4.534 0.167 6.574 find_stability 4.631 0.065 6.419 CORE_subcluster 4.581 0.057 6.422 rand_index 4.518 0.070 6.205 PCA 4.176 0.069 7.529 bootstrap_prediction 3.933 0.114 7.241 reformat_LASSO 3.344 0.090 6.194 summary_deviance 3.118 0.091 5.736 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/scGPS.Rcheck/00check.log’ for details.
scGPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scGPS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘scGPS’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dist_mat_cpp.cpp -o dist_mat_cpp.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dist_parallel_cpp.cpp -o dist_parallel_cpp.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils_rcpp.cpp -o utils_rcpp.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o scGPS.so RcppExports.o dist_mat_cpp.o dist_parallel_cpp.o utils_rcpp.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (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(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 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 10.530 0.641 19.801
scGPS.Rcheck/scGPS-Ex.timings
name | user | system | elapsed | |
CORE_bagging | 10.400 | 0.174 | 17.045 | |
CORE_clustering | 4.732 | 0.064 | 6.613 | |
CORE_subcluster | 4.581 | 0.057 | 6.422 | |
PCA | 4.176 | 0.069 | 7.529 | |
PrinComp_cpp | 0.162 | 0.005 | 0.299 | |
annotate_clusters | 39.145 | 1.515 | 72.492 | |
bootstrap_parallel | 0.578 | 0.020 | 1.074 | |
bootstrap_prediction | 3.933 | 0.114 | 7.241 | |
calcDist | 0.424 | 0.442 | 1.541 | |
calcDistArma | 0.000 | 0.000 | 0.001 | |
clustering | 4.534 | 0.167 | 6.574 | |
clustering_bagging | 8.967 | 0.118 | 14.515 | |
distvec | 0.000 | 0.001 | 0.001 | |
find_markers | 85.908 | 1.016 | 152.766 | |
find_optimal_stability | 4.780 | 0.090 | 6.821 | |
find_stability | 4.631 | 0.065 | 6.419 | |
mean_cpp | 0.002 | 0.001 | 0.006 | |
new_scGPS_object | 0.384 | 0.021 | 0.720 | |
new_summarized_scGPS_object | 0.027 | 0.008 | 0.061 | |
plot_CORE | 4.741 | 0.070 | 6.589 | |
plot_optimal_CORE | 5.550 | 0.092 | 8.106 | |
plot_reduced | 6.357 | 0.133 | 11.084 | |
predicting | 1.338 | 0.060 | 2.459 | |
rand_index | 4.518 | 0.070 | 6.205 | |
rcpp_Eucl_distance_NotPar | 0.016 | 0.001 | 0.029 | |
rcpp_parallel_distance | 0.162 | 0.003 | 0.292 | |
reformat_LASSO | 3.344 | 0.090 | 6.194 | |
sub_clustering | 0.104 | 0.005 | 0.180 | |
subset_cpp | 0.962 | 0.036 | 1.756 | |
summary_accuracy | 1.806 | 0.045 | 3.315 | |
summary_deviance | 3.118 | 0.091 | 5.736 | |
summary_prediction_lasso | 1.845 | 0.052 | 3.443 | |
summary_prediction_lda | 1.888 | 0.051 | 3.458 | |
tSNE | 5.585 | 0.106 | 10.142 | |
top_var | 1.087 | 0.035 | 1.960 | |
tp_cpp | 0.167 | 0.008 | 0.312 | |
training | 0.754 | 0.020 | 1.389 | |
var_cpp | 0.004 | 0.001 | 0.008 | |