Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:43 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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" | 4415 |
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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOSim.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOSim_2.1.0.tar.gz |
StartedAt: 2024-08-26 21:55:19 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 22:10:43 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 924.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MOSim.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOSim.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOSim_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 6.7Mb 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 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 80.117 5.297 85.882 omicSettings 71.649 6.205 78.252 omicSim 70.149 7.169 77.902 plotProfile 61.980 6.804 69.230 omicResults 55.756 5.661 61.750 mosim 54.472 5.259 60.137 experimentalDesign 54.945 4.760 60.089 sc_mosim 43.270 0.991 44.475 sc_omicResults 38.182 0.491 38.831 sc_omicSettings 37.620 0.455 38.224 make_cluster_patterns 18.978 0.125 19.204 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck/00check.log’ for details.
MOSim.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MOSim ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MOSim’ ... ** 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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Random_number.cpp -o Random_number.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o MOSim.so Random_number.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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-apple-darwin20 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 0.440 0.100 0.527
MOSim.Rcheck/MOSim-Ex.timings
name | user | system | elapsed | |
calculate_mean_per_list_df | 0.006 | 0.001 | 0.007 | |
check_patterns | 0.011 | 0.001 | 0.013 | |
discretize | 80.117 | 5.297 | 85.882 | |
experimentalDesign | 54.945 | 4.760 | 60.089 | |
make_cluster_patterns | 18.978 | 0.125 | 19.204 | |
match_gene_regulator | 0.025 | 0.001 | 0.025 | |
match_gene_regulator_cluster | 0.064 | 0.001 | 0.064 | |
mosim | 54.472 | 5.259 | 60.137 | |
omicData | 3.868 | 0.073 | 3.956 | |
omicResults | 55.756 | 5.661 | 61.750 | |
omicSettings | 71.649 | 6.205 | 78.252 | |
omicSim | 70.149 | 7.169 | 77.902 | |
plotProfile | 61.980 | 6.804 | 69.230 | |
sc_mosim | 43.270 | 0.991 | 44.475 | |
sc_omicData | 0.936 | 0.027 | 0.968 | |
sc_omicResults | 38.182 | 0.491 | 38.831 | |
sc_omicSettings | 37.620 | 0.455 | 38.224 | |
sc_param_estimation | 0.208 | 0.012 | 0.221 | |