Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-04-13 12:08:22 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for mosbi on machv2


To the developers/maintainers of the mosbi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mosbi.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1198/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mosbi 1.0.3  (landing page)
Tim Daniel Rose
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/mosbi
git_branch: RELEASE_3_14
git_last_commit: fa15c49
git_last_commit_date: 2022-02-01 03:09:20 -0400 (Tue, 01 Feb 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mosbi
Version: 1.0.3
Command: _R_CHECK_FORCE_SUGGESTS_=0 /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mosbi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mosbi_1.0.3.tar.gz
StartedAt: 2022-04-12 15:44:16 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 15:45:04 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 48.2 seconds
RetCode: 0
Status:   OK  
CheckDir: mosbi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   _R_CHECK_FORCE_SUGGESTS_=0 /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mosbi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mosbi_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/mosbi.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mosbi/DESCRIPTION’ ... OK
* this is package ‘mosbi’ version ‘1.0.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘runibic’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mosbi’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘get_communities’
* 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 ... NOTE
GNU make is a SystemRequirements.
* 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
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/mosbi.Rcheck/00check.log’
for details.



Installation output

mosbi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mosbi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘mosbi’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c attr_graph.cpp -o attr_graph.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c attributeConnector.cpp -o attributeConnector.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c attribute_overlap.cpp -o attribute_overlap.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bicluster_methods.cpp -o bicluster_methods.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost_graph.cpp -o boost_graph.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost_write.cpp -o boost_write.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c distance_matrix.cpp -o distance_matrix.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c extractBF.cpp -o extractBF.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c extractQUBIC2.cpp -o extractQUBIC2.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c full_graph.cpp -o full_graph.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c misc.cpp -o misc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c network_edge_strength.cpp -o network_edge_strength.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sample_biclusters.cpp -o sample_biclusters.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c write_matrix.cpp -o write_matrix.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mosbi.so RcppExports.o attr_graph.o attributeConnector.o attribute_overlap.o bicluster_methods.o boost_graph.o boost_write.o distance_matrix.o extractBF.o extractQUBIC2.o full_graph.o misc.o network_edge_strength.o sample_biclusters.o write_matrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-mosbi/00new/mosbi/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** 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 (mosbi)

Tests output

mosbi.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(mosbi)

Attaching package: 'mosbi'

The following object is masked from 'package:testthat':

    has_names

> 
> test_check("mosbi")
6 6
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
  1.480   0.148   1.604 

Example timings

mosbi.Rcheck/mosbi-Ex.timings

nameusersystemelapsed
NoBFBiclusters0.0000.0000.001
algohistogram0.0020.0010.002
apply_threshold-bicluster_net-method0.0000.0000.001
apply_threshold-cooccurrence_net-method0.0000.0000.001
apply_threshold000
attr_overlap000
attributeConnector000
attribute_graph000
bicluster-class0.0040.0010.005
bicluster_heatmap-bicluster-matrix-method0.0390.0010.040
bicluster_heatmap0.0110.0010.013
bicluster_net-class0.0030.0010.003
bicluster_net_to_igraph-bicluster_net-method0.0000.0010.001
bicluster_net_to_igraph000
bicluster_network0.0010.0000.001
bicluster_to_matrix0.0010.0010.001
check_names0.0000.0010.001
clean_bicluster_list0.0030.0010.005
colhistogram0.0000.0010.001
cooccurrence_net-class0.0020.0000.003
cooccurrence_net_to_igraph-cooccurrence_net-method000
cooccurrence_net_to_igraph000
cpp_matrix_subsetting0.0010.0000.001
detect_elements0.0010.0000.001
dim-bicluster-method0.0010.0000.001
distance_matrix0.0020.0010.002
ensemble_biclusters0.0020.0010.001
feature_louvain_overlap0.0010.0000.000
feature_network0.0010.0000.001
filter_bicluster_size0.0020.0000.002
filter_biclusters0.0010.0000.002
filter_matrix0.0000.0000.001
filter_subsets0.0020.0010.003
full_graph0.0010.0000.002
getAkmbiclustClusters000
getBFCluster0.0000.0010.000
getBicAREbiclusters000
getBiclustClusters0.0010.0000.000
getBiclustpyClusters0.0000.0010.000
getFabiaClusters0.0010.0000.001
getIsaClusters0.0010.0000.001
getQUBIC2biclusters0.0010.0000.001
get_adjacency-bicluster_net-method000
get_adjacency000
get_algorithms0.0010.0000.001
get_bic_net_algorithms-bicluster_net-method000
get_bic_net_algorithms000
get_biclusters0.0010.0000.000
get_louvain_communities-bicluster_net-method000
get_louvain_communities-cooccurrence_net-method000
get_louvain_communities0.0000.0000.001
getallBFClusters0.0000.0000.001
has_names0.0010.0000.001
is_subset_or_identical0.0010.0000.001
network_edge_strength0.0000.0000.001
network_edge_strength_float000
node_size000
occurance_matrix0.0010.0010.000
occurance_table0.0010.0000.000
p_overlap0.0010.0000.001
p_overlap_2d0.0010.0010.000
p_overlap_2d_higher0.0010.0000.000
p_overlap_higher000
plot-bicluster_net-missing-method0.0000.0000.001
plot-cooccurrence_net-missing-method0.0000.0000.001
plot_algo_network0.0010.0010.000
plot_piechart_bicluster_network0.0010.0000.000
randomize_matrix0.0010.0000.001
replace_threshold000
replace_values0.0000.0010.001
replace_values_float0.0010.0010.001
rowhistogram000
run_akmbiclust000
run_bimax000
run_cc0.0000.0000.001
run_fabia000
run_isa000
run_plaid0.0010.0000.001
run_qubic0.0010.0010.000
run_quest0.0010.0000.000
run_spectral0.0010.0000.001
run_unibic0.0010.0010.001
run_xmotifs0.0010.0000.000
sample_biclusters0.0010.0000.001
select_biclusters_from_bicluster_network-bicluster_net-list-method0.0010.0000.001
select_biclusters_from_bicluster_network0.0010.0010.000
set_bicluster_names0.0020.0010.002
similarity_matrix0.0010.0010.001
transpose_bicluster0.0010.0010.002
validate_bicluster0.0010.0010.002
write_graphml0.0000.0000.001
write_matrix0.0000.0000.001
zero_subsetting0.0000.0000.001