===============================
R CMD BUILD
===============================
* checking for file ‘monarchr/DESCRIPTION’ ... OK
* preparing ‘monarchr’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘monarchr_2.99.0.tar.gz’
===============================
BiocCheckGitClone('monarchr')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4139/monarchr_20260504170452/monarchr
→ BiocVersion: 3.23
→ Package: monarchr
→ PackageVersion: 2.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4139/monarchr_20260504170452/monarchr.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4139/monarchr_20260504170452/monarchr
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for remote package usage...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4139/monarchr_20260504170452/monarchr.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-04 17:06:00 UTC
* using option ‘--no-vignettes’
* checking for file ‘monarchr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘monarchr’ version ‘2.99.0’
* 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 ‘monarchr’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking whether startup messages can be suppressed ... [2s/2s] OK
* checking use of S3 registration ... 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 ... [9s/9s] NOTE
expand_neo4j_engine: warning in suppressMessages(result_cumulative <-
graph_join(result_cumulative, result), class = "message"): partial
argument match of 'class' to 'classes'
fetch_nodes.neo4j_engine: warning in suppressMessages(result_cumulative
<- graph_join(result_cumulative, result), class = "message"): partial
argument match of 'class' to 'classes'
transitive_closure: warning in roll_down(id, include_self = FALSE,
predicate = predicate): partial argument match of 'predicate' to
'predicates'
color_cats: no visible global function definition for ‘setNames’
direction_fetch_internal: no visible binding for global variable
‘subject’
direction_fetch_internal: no visible binding for global variable
‘object’
direction_fetch_internal: no visible binding for global variable
‘predicate’
direction_fetch_internal: no visible binding for global variable ‘id’
direction_fetch_internal: no visible binding for global variable
‘category’
example_graph.file_engine: no visible binding for global variable
‘predicate’
example_graph.file_engine: no visible binding for global variable ‘to’
example_graph.file_engine: no visible binding for global variable
‘from’
example_graph.file_engine: no visible binding for global variable ‘id’
example_graph.file_engine: no visible binding for global variable
‘category’
example_graph.file_engine : <anonymous>: no visible global function
definition for ‘head’
example_graph.file_engine : <anonymous>: no visible binding for global
variable ‘subject’
example_graph.file_engine : <anonymous>: no visible binding for global
variable ‘object’
example_graph.file_engine : <anonymous>: no visible binding for global
variable ‘to’
example_graph.file_engine : <anonymous>: no visible binding for global
variable ‘from’
example_graph.neo4j_engine: no visible binding for global variable
‘category’
expand_neo4j_engine: no visible global function definition for ‘head’
expand_neo4j_engine: no visible binding for global variable ‘subject’
expand_neo4j_engine: no visible binding for global variable ‘predicate’
expand_neo4j_engine: no visible binding for global variable ‘object’
expand_neo4j_engine: no visible binding for global variable ‘id’
expand_neo4j_engine: no visible binding for global variable ‘category’
explode.tbl_kgx : <anonymous>: no visible binding for global variable
‘id’
fetch_nodes.file_engine: no visible binding for global variable ‘id’
graph_centrality: no visible global function definition for ‘:=’
graph_semsim: no visible global function definition for ‘:=’
graph_sparsity: no visible global function definition for ‘is’
kg_edge_weights: no visible global function definition for ‘:=’
kg_join.tbl_kgx: no visible binding for global variable ‘to’
kg_join.tbl_kgx: no visible binding for global variable ‘from’
kg_join.tbl_kgx : fill_edges: no visible binding for global variable
‘id’
kg_join.tbl_kgx : fill_edges: no visible binding for global variable
‘idx’
kg_join.tbl_kgx: no visible binding for global variable ‘edge_idx’
kg_join.tbl_kgx: no visible binding for global variable ‘.’
kg_join.tbl_kgx: no visible binding for global variable ‘idx’
monarch_semsim: no visible binding for global variable ‘id’
plot.tbl_kgx: no visible binding for global variable ‘pcategory’
plot.tbl_kgx: no visible binding for global variable ‘namespace’
plot.tbl_kgx: no visible binding for global variable ‘predicate’
plot.tbl_kgx: no visible binding for global variable
‘primary_knowledge_source’
plot.tbl_kgx: no visible binding for global variable ‘name’
plot.tbl_kgx: no visible global function definition for ‘:=’
plot.tbl_kgx: no visible binding for global variable ‘plot_name’
plot.tbl_kgx: no visible binding for global variable ‘id’
roll: no visible binding for global variable ‘predicate’
summarize_neighborhood_edges_neo4j_engine: no visible binding for
global variable ‘query_pcategory’
summarize_neighborhood_edges_neo4j_engine: no visible binding for
global variable ‘query_category’
summarize_neighborhood_edges_neo4j_engine: no visible binding for
global variable ‘predicate’
summarize_neighborhood_edges_neo4j_engine: no visible binding for
global variable ‘result_pcategory’
summarize_neighborhood_edges_neo4j_engine: no visible binding for
global variable ‘result_category’
summarize_neighborhood_nodes_neo4j_engine: no visible binding for
global variable ‘pcategory’
summary.file_engine: no visible binding for global variable ‘category’
summary.file_engine: no visible binding for global variable ‘predicate’
transfer: no visible binding for global variable ‘predicate’
transfer : <anonymous>: no visible binding for global variable ‘id’
transitive_closure: no visible binding for global variable ‘id’
transitive_closure: no visible binding for global variable
‘downstream_nodes’
transitive_closure: no visible binding for global variable ‘subject’
transitive_closure: no visible binding for global variable ‘object’
transitive_closure: no visible binding for global variable
‘primary_knowledge_source’
transitive_closure: no visible binding for global variable ‘index’
transitive_closure: no visible binding for global variable ‘edge_key’
transitive_query_internal: no visible binding for global variable
‘predicate’
transitive_query_internal: no visible binding for global variable ‘id’
transitive_query_internal: no visible binding for global variable
‘depth’
transitive_query_internal: no visible binding for global variable
‘category’
Undefined global functions or variables:
. := category depth downstream_nodes edge_idx edge_key from head id
idx index is name namespace object pcategory plot_name predicate
primary_knowledge_source query_category query_pcategory
result_category result_pcategory setNames subject to
Consider adding
importFrom("methods", "is")
importFrom("stats", "setNames")
importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [74s/174s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
expand_n 19.618 0.095 19.714
layout_umap 8.369 0.062 8.432
monarch_semsim 2.359 0.004 20.050
expand 1.415 0.042 21.371
load_kgx 0.671 0.020 19.760
save_kgx 0.624 0.019 14.381
fetch_nodes 0.562 0.011 6.242
summarize_neighborhood 0.254 0.007 6.446
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [27s/211s]
[27s/211s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
Expected: 8
Missing: 8
── Failure ('test-expand.monarch_engine.R:98:5'): expand works as expected ─────
Expected `4 + -2:2` to contain all values in `nrow(edges_df)`.
Actual: 2, 3, 4, 5, 6
Expected: 7
Missing: 7
── Failure ('test-expand.monarch_engine.R:109:5'): expand works as expected ────
Expected `4 + -2:2` to contain all values in `nrow(nodes_df)`.
Actual: 2, 3, 4, 5, 6
Expected: 7
Missing: 7
── Failure ('test-expand.monarch_engine.R:110:5'): expand works as expected ────
Expected `3 + -2:2` to contain all values in `nrow(edges_df)`.
Actual: 1, 2, 3, 4, 5
Expected: 6
Missing: 6
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 193 ]
Error:
! Test failures.
Execution halted
* 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 ... [4s/4s] OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4139/monarchr_20260504170452/monarchr.Rcheck/00check.log’
for details.
===============================
BiocCheck('monarchr_2.99.0.tar.gz')
===============================
── Installing monarchr ─────────────────────────────────────────────────────────
✔ Package installed successfully
── monarchr session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNXNGh1/file22ffab11078dd6/monarchr
→ BiocVersion: 3.23
→ Package: monarchr
→ PackageVersion: 2.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4139/monarchr_20260504170452/monarchr.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpNXNGh1/file22ffab11078dd6/monarchr
→ installDir: /tmp/RtmpNXNGh1/file22ffab6ffffc7a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on monarchr ───────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
! WARNING: New package x version starting with non-zero value (e.g., 1.y.z,
2.y.z); got ‘2.99.0’.
* Checking R version dependency...
i NOTE: Update R version dependency from 4.4.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• engine_preferences.Rmd
• ...
• visualizing_kgs.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of monarchr...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 12 times)
• suppressMessages() in R/cypher_query.neo4j_engine.R (line 233, column 13)
• ...
• suppressMessages() in R/transitive_reduction.R (line 87, column 5)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 23
functions greater than 50 lines.
The longest 5 functions are:
• expand_neo4j_engine() (R/expand_neo4j_engine.R): 202 lines
• ...
• file_engine() (R/file_engine.R): 90 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 299 lines (5%) are > 80 characters long.
First few lines:
• R/cypher_query.neo4j_engine.R#L14 if (all(unlist(lapply(x, functio ...
• ...
• vignettes/visualizing_kgs.Rmd#L111 <center>![A screenshot of Cytoscape
with ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | i 5 NOTES
i See the monarchr.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.