Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:30 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 282/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ccfindR 1.22.0 (landing page) Jun Woo
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the ccfindR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ccfindR.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ccfindR |
Version: 1.22.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ccfindR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ccfindR_1.22.0.tar.gz |
StartedAt: 2023-11-02 09:02:14 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 09:07:32 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 317.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ccfindR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ccfindR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ccfindR_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ccfindR.Rcheck’ * using R version 4.3.1 (2023-06-16) * 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 * using option ‘--no-vignettes’ * checking for file ‘ccfindR/DESCRIPTION’ ... OK * this is package ‘ccfindR’ version ‘1.22.0’ * 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 ‘ccfindR’ 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 7.7Mb sub-directories of 1Mb or more: libs 6.2Mb * 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed assignCelltype 17.890 3.148 21.305 factorize 9.405 0.576 10.725 newick 4.223 0.852 6.027 plot_tree 3.585 0.977 5.083 vb_factorize 3.650 0.520 5.789 * 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-3.18-bioc/meat/ccfindR.Rcheck/00check.log’ for details.
ccfindR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL ccfindR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘ccfindR’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c vbnmf_update.cpp -o vbnmf_update.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o ccfindR.so RcppExports.o vbnmf_update.o -lgsl -lgslcblas -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-ccfindR/00new/ccfindR/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help Loading required namespace: ccfindR *** 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 (ccfindR)
ccfindR.Rcheck/ccfindR-Ex.timings
name | user | system | elapsed | |
assignCelltype | 17.890 | 3.148 | 21.305 | |
basis-set-scNMFSet-method | 0.323 | 0.000 | 0.323 | |
basis-set | 0.242 | 0.000 | 0.243 | |
basis | 0.255 | 0.028 | 0.283 | |
build_tree | 3.568 | 0.004 | 3.581 | |
cell_map | 0.596 | 0.005 | 0.613 | |
cluster_id | 3.522 | 0.000 | 3.529 | |
coeff-set-scNMFSet-method | 0.241 | 0.000 | 0.242 | |
coeff-set | 0.260 | 0.000 | 0.264 | |
coeff | 0.285 | 0.947 | 2.099 | |
colData-scNMFSet-method | 0.279 | 0.017 | 0.320 | |
colData-set-scNMFSet-ANY-method | 0.273 | 0.024 | 0.300 | |
counts-scNMFSet-method | 0.211 | 0.012 | 0.223 | |
counts-set-scNMFSet-method | 0.262 | 0.004 | 0.266 | |
factorize | 9.405 | 0.576 | 10.725 | |
feature_map | 0.439 | 0.003 | 0.449 | |
filter_cells | 0.293 | 0.008 | 0.302 | |
filter_genes | 0.326 | 0.004 | 0.331 | |
gene_map | 0.453 | 0.000 | 0.454 | |
measure-set-scNMFSet-method | 0.258 | 0.000 | 0.259 | |
measure-set | 0.258 | 0.000 | 0.258 | |
measure | 0.270 | 0.001 | 0.272 | |
meta_gene.cv | 3.542 | 0.011 | 3.578 | |
meta_genes | 0.451 | 0.003 | 0.457 | |
newick | 4.223 | 0.852 | 6.027 | |
normalize_count | 0.283 | 0.000 | 0.286 | |
optimal_rank | 3.474 | 0.007 | 3.489 | |
plot_genes | 0.218 | 0.000 | 0.218 | |
plot_tree | 3.585 | 0.977 | 5.083 | |
ranks-set-scNMFSet-method | 0.292 | 0.000 | 0.293 | |
ranks-set | 0.293 | 0.000 | 0.293 | |
ranks | 0.271 | 0.000 | 0.271 | |
read_10x | 0.674 | 0.063 | 0.883 | |
remove_zeros | 0.296 | 0.690 | 1.779 | |
rename_tips | 3.557 | 0.032 | 3.600 | |
rowData-scNMFSet-method | 0.227 | 0.000 | 0.228 | |
scNMFSet-class | 0.685 | 0.000 | 0.688 | |
scNMFSet | 0.208 | 0.000 | 0.209 | |
show-scNMFSet-method | 0.213 | 0.000 | 0.214 | |
simulate_data | 0.219 | 0.000 | 0.220 | |
simulate_whx | 3.648 | 0.693 | 4.689 | |
vb_factorize | 3.650 | 0.520 | 5.789 | |
visualize_clusters | 1.240 | 0.011 | 1.272 | |
write_10x | 0.234 | 0.000 | 0.238 | |
write_meta | 3.553 | 0.016 | 3.575 | |