Quan Nguyen
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/scGPS |
| Branch: RELEASE_3_10 |
| Last Commit: ccc1da7 |
| Last Changed Date: 2019-10-29 13:11:47 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:15:58 -0400 (Wed, 15 Apr 2020).
| Package 1533/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scGPS 1.0.0 Quan Nguyen
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: scGPS |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scGPS.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scGPS_1.0.0.tar.gz |
| StartedAt: 2020-04-15 06:43:04 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:49:38 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 393.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scGPS.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scGPS.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scGPS_1.0.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/scGPS.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scGPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scGPS’ version ‘1.0.0’
* 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
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
data 2.0Mb
libs 2.9Mb
* 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 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
annotate_clusters 17.056 0.044 17.424
CORE_bagging 15.800 0.188 14.152
clustering_bagging 14.004 0.080 12.301
plot_optimal_CORE 9.644 0.052 7.924
tSNE 8.528 0.048 8.744
plot_reduced 8.440 0.060 8.880
find_optimal_stability 8.164 0.040 6.186
CORE_clustering 7.732 0.068 5.945
clustering 7.656 0.056 5.814
rand_index 7.636 0.040 5.776
CORE_subcluster 7.544 0.032 5.852
find_stability 7.060 0.060 5.188
plot_CORE 6.972 0.060 5.417
reformat_LASSO 6.420 0.108 6.628
summary_deviance 6.300 0.120 6.514
find_markers 5.840 0.100 6.116
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/scGPS.Rcheck/00check.log’
for details.
scGPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL scGPS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘scGPS’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include -fpic -g -O2 -Wall -c dist_mat_cpp.cpp -o dist_mat_cpp.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include -fpic -g -O2 -Wall -c dist_parallel_cpp.cpp -o dist_parallel_cpp.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include -fpic -g -O2 -Wall -c utils_rcpp.cpp -o utils_rcpp.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o scGPS.so RcppExports.o dist_mat_cpp.o dist_parallel_cpp.o utils_rcpp.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.10-bioc/R/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(scGPS)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: dynamicTreeCut
Loading required package: SingleCellExperiment
>
> test_check("scGPS")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
13.948 0.520 14.672
scGPS.Rcheck/scGPS-Ex.timings
| name | user | system | elapsed | |
| CORE_bagging | 15.800 | 0.188 | 14.152 | |
| CORE_clustering | 7.732 | 0.068 | 5.945 | |
| CORE_subcluster | 7.544 | 0.032 | 5.852 | |
| PCA | 4.468 | 0.060 | 4.549 | |
| PrinComp_cpp | 0.228 | 0.000 | 0.231 | |
| annotate_clusters | 17.056 | 0.044 | 17.424 | |
| bootstrap_parallel | 0.176 | 0.000 | 0.179 | |
| bootstrap_prediction | 4.572 | 0.104 | 4.775 | |
| calcDist | 0.388 | 0.212 | 0.607 | |
| calcDistArma | 0.004 | 0.000 | 0.001 | |
| clustering | 7.656 | 0.056 | 5.814 | |
| clustering_bagging | 14.004 | 0.080 | 12.301 | |
| distvec | 0.000 | 0.000 | 0.001 | |
| find_markers | 5.840 | 0.100 | 6.116 | |
| find_optimal_stability | 8.164 | 0.040 | 6.186 | |
| find_stability | 7.060 | 0.060 | 5.188 | |
| mean_cpp | 0.004 | 0.000 | 0.003 | |
| new_scGPS_object | 0.140 | 0.000 | 0.142 | |
| new_summarized_scGPS_object | 0.020 | 0.000 | 0.021 | |
| plot_CORE | 6.972 | 0.060 | 5.417 | |
| plot_optimal_CORE | 9.644 | 0.052 | 7.924 | |
| plot_reduced | 8.44 | 0.06 | 8.88 | |
| predicting | 1.612 | 0.032 | 1.658 | |
| rand_index | 7.636 | 0.040 | 5.776 | |
| rcpp_Eucl_distance_NotPar | 0.024 | 0.000 | 0.024 | |
| rcpp_parallel_distance | 0.228 | 0.000 | 0.284 | |
| reformat_LASSO | 6.420 | 0.108 | 6.628 | |
| sub_clustering | 0.144 | 0.012 | 0.122 | |
| subset_cpp | 0.220 | 0.012 | 0.240 | |
| summary_accuracy | 3.264 | 0.052 | 3.460 | |
| summary_deviance | 6.300 | 0.120 | 6.514 | |
| summary_prediction_lasso | 3.224 | 0.056 | 3.379 | |
| summary_prediction_lda | 3.088 | 0.060 | 3.289 | |
| tSNE | 8.528 | 0.048 | 8.744 | |
| top_var | 0.164 | 0.020 | 0.186 | |
| tp_cpp | 0.240 | 0.000 | 0.239 | |
| training | 0.504 | 0.000 | 0.508 | |
| var_cpp | 0.004 | 0.000 | 0.006 | |