Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:39 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1297/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MOSim 2.1.0 (landing page) Sonia Tarazona
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the MOSim package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MOSim.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: MOSim |
Version: 2.1.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MOSim.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MOSim_2.1.0.tar.gz |
StartedAt: 2024-08-21 01:09:25 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 01:25:21 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 956.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MOSim.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MOSim.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MOSim_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘MOSim/DESCRIPTION’ ... OK * this is package ‘MOSim’ version ‘2.1.0’ * 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 ‘MOSim’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘dplyr::count’ by ‘matrixStats::count’ when loading ‘MOSim’ See ‘/home/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: data 5.8Mb * 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 whether startup messages can be suppressed ... 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 make_association_dataframe : keep_remaining: no visible binding for global variable ‘Freq.a’ make_association_dataframe : keep_remaining: no visible binding for global variable ‘Freq.ao’ make_association_dataframe : keep_remaining: no visible binding for global variable ‘cluster’ make_association_dataframe : keep_remaining: no visible binding for global variable ‘Freq’ make_association_dataframe : keep_remaining2: no visible binding for global variable ‘Freq.a’ make_association_dataframe : keep_remaining2: no visible binding for global variable ‘Freq.ao’ make_association_dataframe : keep_remaining2: no visible binding for global variable ‘cluster’ make_association_dataframe : keep_remaining2: no visible binding for global variable ‘Freq’ make_association_dataframe: no visible binding for global variable ‘Peak_ID’ make_association_dataframe: no visible binding for global variable ‘Gene_ID’ Undefined global functions or variables: Freq Freq.a Freq.ao Gene_ID Peak_ID cluster * checking Rd files ... NOTE checkRd: (-1) TF_human.Rd:12: Lost braces; missing escapes or markup? 12 | @source {https://tflink.net/} | ^ checkRd: (-1) associationList.Rd:14: Lost braces; missing escapes or markup? 14 | @source {Created in-house to serve as an example} | ^ checkRd: (-1) sc_mosim.Rd:94: Lost braces; missing escapes or markup? 94 | {https://tflink.net/}} | ^ checkRd: (-1) scatac.Rd:14-15: Lost braces 14 | @source {https://github.com/satijalab/seurat-data, we took 11 cells | ^ checkRd: (-1) scrna.Rd:14-15: Lost braces 14 | @source {https://github.com/satijalab/seurat-data, we took 11 cells | ^ checkRd: (-1) scrna.Rd:23-28: Lost braces 23 | for (cell_type in unique_cell_types) { | ^ * 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 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 discretize 56.548 1.256 57.805 omicSettings 51.313 0.567 51.881 omicSim 48.264 0.340 48.605 plotProfile 47.029 0.236 47.267 sc_mosim 38.926 0.252 39.179 omicResults 35.852 0.264 36.116 experimentalDesign 35.519 0.352 35.871 sc_omicSettings 34.938 0.208 35.147 mosim 34.296 0.351 34.648 sc_omicResults 33.484 0.200 33.684 make_cluster_patterns 11.743 0.020 11.764 * 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: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck/00check.log’ for details.
MOSim.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MOSim ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘MOSim’ ... ** 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/cpp11/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c Random_number.cpp -o Random_number.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o MOSim.so Random_number.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-MOSim/00new/MOSim/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘dplyr::count’ by ‘matrixStats::count’ when loading ‘MOSim’ Creating a new generic function for ‘simulate’ in package ‘MOSim’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘dplyr::count’ by ‘matrixStats::count’ when loading ‘MOSim’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘dplyr::count’ by ‘matrixStats::count’ when loading ‘MOSim’ ** testing if installed package keeps a record of temporary installation path * DONE (MOSim)
MOSim.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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(MOSim) > > #test_check("MOSim") > > proc.time() user system elapsed 0.314 0.039 0.344
MOSim.Rcheck/MOSim-Ex.timings
name | user | system | elapsed | |
calculate_mean_per_list_df | 0.005 | 0.000 | 0.006 | |
check_patterns | 0.011 | 0.000 | 0.010 | |
discretize | 56.548 | 1.256 | 57.805 | |
experimentalDesign | 35.519 | 0.352 | 35.871 | |
make_cluster_patterns | 11.743 | 0.020 | 11.764 | |
match_gene_regulator | 0.018 | 0.000 | 0.019 | |
match_gene_regulator_cluster | 0.046 | 0.000 | 0.046 | |
mosim | 34.296 | 0.351 | 34.648 | |
omicData | 3.233 | 0.061 | 3.293 | |
omicResults | 35.852 | 0.264 | 36.116 | |
omicSettings | 51.313 | 0.567 | 51.881 | |
omicSim | 48.264 | 0.340 | 48.605 | |
plotProfile | 47.029 | 0.236 | 47.267 | |
sc_mosim | 38.926 | 0.252 | 39.179 | |
sc_omicData | 0.629 | 0.000 | 0.629 | |
sc_omicResults | 33.484 | 0.200 | 33.684 | |
sc_omicSettings | 34.938 | 0.208 | 35.147 | |
sc_param_estimation | 0.135 | 0.000 | 0.136 | |