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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1313/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOSim 2.2.0  (landing page)
Sonia Tarazona
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/MOSim
git_branch: RELEASE_3_20
git_last_commit: b7b8075
git_last_commit_date: 2024-10-29 10:39:30 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for MOSim on merida1

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.

raw results


Summary

Package: MOSim
Version: 2.2.0
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_2.2.0.tar.gz
StartedAt: 2024-12-20 06:19:35 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:47:45 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1689.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MOSim.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MOSim/DESCRIPTION’ ... OK
* this is package ‘MOSim’ version ‘2.2.0’
* 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            154.085  6.020 165.596
omicSettings          143.198  5.725 159.034
omicSim               138.003  6.609 150.978
plotProfile           132.513  6.642 146.135
omicResults           107.891  5.039 119.761
experimentalDesign    107.732  4.702 115.488
mosim                 104.778  5.157 114.282
sc_mosim               58.307  1.000  61.827
sc_omicSettings        47.844  0.634  57.252
sc_omicResults         47.261  0.507  49.751
make_cluster_patterns  37.953  0.277  42.429
omicData                6.721  0.074   7.137
* 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.


Installation output

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)

Tests output

MOSim.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 
  0.748   0.145   0.869 

Example timings

MOSim.Rcheck/MOSim-Ex.timings

nameusersystemelapsed
calculate_mean_per_list_df0.0080.0020.011
check_patterns0.0180.0010.021
discretize154.085 6.020165.596
experimentalDesign107.732 4.702115.488
make_cluster_patterns37.953 0.27742.429
match_gene_regulator0.0450.0030.054
match_gene_regulator_cluster0.1100.0030.119
mosim104.778 5.157114.282
omicData6.7210.0747.137
omicResults107.891 5.039119.761
omicSettings143.198 5.725159.034
omicSim138.003 6.609150.978
plotProfile132.513 6.642146.135
sc_mosim58.307 1.00061.827
sc_omicData1.1880.0261.272
sc_omicResults47.261 0.50749.751
sc_omicSettings47.844 0.63457.252
sc_param_estimation0.2650.0120.297