Validation Report - brainGraph@3.1.0
Context
This report is fully automated and builds on rhub/ref-image image. Documents the installation of this package on an open source R environment, focusing on:
- Installation environment description
- Testing coverage
It is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful.
Package brainGraph
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 98 |
| has_vignettes | 0 |
| export_help | 98 |
| has_website | TRUE |
| has_maintainer | Christopher G. Watson cgwatson@bu.edu |
| bugs_status | scraping bug reports fromm BugReports host ‘google’ not implemented |
| has_source_control | https://github.com/cwatson/brainGraph |
| has_bug_reports_url | 1 |
| downloads_1yr | 6835 |
| reverse_dependencies | 3 |
| has_examples | 1 |
| dependencies | 12 |
| license | GPL-3 |
Package general assessment: Coverage, check results, size, download the last year, reverse dependencies and number of dependencies.
Dependencies
Overall the package has these dependencies:
| package | type | |
|---|---|---|
| 1 | igraph (>= 1.2.4) | Depends |
| 2 | abind | Imports |
| 3 | data.table (>= 1.12.4) | Imports |
| 4 | doParallel | Imports |
| 5 | foreach | Imports |
| 6 | grid | Imports |
| 7 | lattice | Imports |
| 8 | MASS | Imports |
| 9 | Matrix | Imports |
| 10 | methods | Imports |
| 11 | permute | Imports |
| 12 | parallel | Imports |
Package dependencies
Reverse dependencies
Overall the package has 3 reverse dependencies:
etree, PopulateR, priorCON
Namespace
Overall the package has 98 exported objects. 98 are documented:
analysis_random_graphs aop
TRUE TRUE
apply_thresholds as_atlas
TRUE TRUE
as_brainGraphList bg_to_mediate
TRUE TRUE
brainGraph_boot brainGraph_GLM
TRUE TRUE
brainGraph_GLM_design brainGraph_mediate
TRUE TRUE
brainGraph_permute centr_betw_comm
TRUE TRUE
centr_lev check_sID
TRUE TRUE
coeff_determ coeff_table
TRUE TRUE
coeff_var colMax
TRUE TRUE
colMaxAbs colMin
TRUE TRUE
communicability contract_brainGraph
TRUE TRUE
cor.diff.test corr.matrix
TRUE TRUE
count_homologous count_inter
TRUE TRUE
covratio.bg_GLM create_atlas
TRUE TRUE
create_mats dffits.bg_GLM
TRUE TRUE
diag_sq edge_asymmetry
TRUE TRUE
edge_spatial_dist efficiency
TRUE TRUE
fastLmBG fastLmBG_3d
TRUE TRUE
fastLmBG_3dY fastLmBG_3dY_1p
TRUE TRUE
fastLmBG_f fastLmBG_t
TRUE TRUE
gateway_coeff get_thresholds
TRUE TRUE
get.resid graph_attr_dt
TRUE TRUE
guess_atlas hubness
TRUE TRUE
import_scn inv
TRUE TRUE
is_binary is.brainGraph
TRUE TRUE
is.brainGraphList loo
TRUE TRUE
make_auc_brainGraph make_brainGraph
TRUE TRUE
make_brainGraphList make_ego_brainGraph
TRUE TRUE
make_empty_brainGraph make_intersection_brainGraph
TRUE TRUE
mean_distance_wt mtpc
TRUE TRUE
NBS nregions
TRUE TRUE
pad_zeros part_coeff
TRUE TRUE
partition pinv
TRUE TRUE
plot_brainGraph_multi plot_global
TRUE TRUE
plot_rich_norm plot_vertex_measures
TRUE TRUE
plot_volumetric qr_Q2
TRUE TRUE
qr_R2 randomise
TRUE TRUE
randomise_3d region.names
TRUE TRUE
rich_club_all rich_club_attrs
TRUE TRUE
rich_club_coeff rich_club_norm
TRUE TRUE
rich_core robustness
TRUE TRUE
s_core set_brainGraph_attr
TRUE TRUE
sim.rand.graph.clust sim.rand.graph.hqs
TRUE TRUE
sim.rand.graph.par slicer
TRUE TRUE
small.world symm_mean
TRUE TRUE
symmetrize vertex_attr_dt
TRUE TRUE
vertex_spatial_dist vif.bg_GLM
TRUE TRUE
vulnerability within_module_deg_z_score
TRUE TRUE
write_brainnet xfm.weights
TRUE TRUE Examples
There are 75 help pages with examples, from 75 (100.00 %).
NEWS
The package has NEWS file and it is current.
License
The package uses .
Installation environment
System Info
| Field | Value |
|---|---|
| Image | rhub/ref-image |
| OS | Ubuntu 24.04.1 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-02-15 04:40:46 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
loaded via a namespace (and not attached):
[1] riskreports_0.0.0.9003 compiler_4.4.2 fastmap_1.2.0
[4] cli_3.6.4 htmltools_0.5.8.1 yaml_2.3.10
[7] rmarkdown_2.29 knitr_1.49 jsonlite_1.8.9
[10] xfun_0.50 digest_0.6.37 rlang_1.1.5
[13] evaluate_1.0.3 Platform used:
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"unix" "/" ".so" "X11" "little" "source" ":"
r_arch
"" R’s capabilities:
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TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE FALSE TRUE FALSE TRUE
NLS Rprof profmem cairo ICU long.double
TRUE TRUE TRUE TRUE TRUE TRUE
libcurl
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bzlib
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xz
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libdeflate
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TRE
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readline
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BLAS
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"1.6.43" "8.0" "LIBTIFF, Version 4.5.1" Numerical characteristics of the machine:
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double.max.exp integer.max sizeof.long
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-1.638200e+04 1.638400e+04 Random number generation process:
[1] "Mersenne-Twister" "Inversion" "Rejection" Information about the environment
Environmental and options variables affect how package checks and software in it might behave. Here is the environmental variables when running this report
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