===============================
R CMD BUILD
===============================
* checking for file scToppR/DESCRIPTION ... OK
* preparing scToppR:
* 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 scToppR_0.99.6.tar.gz
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BiocCheckGitClone('scToppR')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3523/f58d6faedad4f21f0ffd0fea5a1daed96b2b9497/scToppR
BiocVersion: 3.23
Package: scToppR
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3523/f58d6faedad4f21f0ffd0fea5a1daed96b2b9497/scToppR.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3523/f58d6faedad4f21f0ffd0fea5a1daed96b2b9497/scToppR
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3523/f58d6faedad4f21f0ffd0fea5a1daed96b2b9497/scToppR/.gitignore'
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck v1.47.1 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3523/f58d6faedad4f21f0ffd0fea5a1daed96b2b9497/scToppR.Rcheck
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file scToppR/DESCRIPTION ... OK
* this is package scToppR version 0.99.6
* 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 ... NOTE
Found the following hidden files and directories:
.styler
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 scToppR 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] 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 ... [6s/6s] NOTE
.sctoppr_dotplot: no visible binding for global variable Category
.sctoppr_dotplot: no visible binding for global variable
GenesInTermInQuery
.sctoppr_dotplot: no visible binding for global variable GenesInTerm
.sctoppr_dotplot: no visible binding for global variable geneRatio
.sctoppr_dotplot: no visible binding for global variable Name
toppBalloon: no visible binding for global variable Category
toppBalloon: no visible binding for global variable QValueFDRBH
toppBalloon: no visible binding for global variable
GenesInTermInQuery
toppBalloon: no visible binding for global variable GenesInTerm
toppBalloon: no visible binding for global variable nlog10_fdr
toppBalloon: no visible binding for global variable Name
toppBalloon: no visible binding for global variable geneRatio
toppFun: no visible binding for global variable genes_submit_cutoff
Undefined global functions or variables:
Category GenesInTerm GenesInTermInQuery Name QValueFDRBH geneRatio
genes_submit_cutoff nlog10_fdr
* 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 ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [28s/53s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
toppFun 19.107 0.199 43.853
toppBalloon 6.018 0.126 6.144
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [23s/94s]
[23s/95s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
Creating Balloon Plot:GeneOntologyMolecularFunction
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 22 ]
Failed tests
Error ('test-toppFun.R:70:5'): toppFun save as xlsx works
<httr2_failure/httr2_error/rlang_error/error/condition>
Error in `httr2::req_perform(httr2::req_body_json(req, list(Symbols = genes)))`: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Failed writing received data to disk/application [toppgene.cchmc.org]
Backtrace:
1. scToppR::toppFun(...) at test-toppFun.R:70:5
2. scToppR:::.get_topp(...)
3. scToppR::get_Entrez(gene_list)
4. httr2::req_perform(httr2::req_body_json(req, list(Symbols = genes)))
5. httr2:::handle_resp(req, resp, error_call = error_call)
6. rlang::cnd_signal(resp)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 22 ]
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 ... [3s/3s] OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3523/f58d6faedad4f21f0ffd0fea5a1daed96b2b9497/scToppR.Rcheck/00check.log
for details.
===============================
BiocCheck('scToppR_0.99.6.tar.gz')
===============================
Installing scToppR
Package installed successfully
scToppR session metadata
sourceDir: /tmp/RtmpPD43BT/file16de13386d6f0a/scToppR
BiocVersion: 3.23
Package: scToppR
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3523/f58d6faedad4f21f0ffd0fea5a1daed96b2b9497/scToppR.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /tmp/RtmpPD43BT/file16de13386d6f0a/scToppR
installDir: /tmp/RtmpPD43BT/file16de134b59b2be
isTarBall: TRUE
platform: unix
Running BiocCheck on scToppR
* 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...
* 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 that Package field matches directory/tarball name...
* 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...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* 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:
differential_expression_airway.Rmd
differential_expression_seurat.Rmd
introduction.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scToppR...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat in R/topp_plot.R (line 296, column 10)
...
cat in R/topp_plot.R (line 312, column 27)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
The longest 5 functions are:
toppFun() (R/toppFun.R): 185 lines
...
.get_topp() (R/toppFun.R): 55 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
Found in files:
toppSave.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
toppSave.Rd
* 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; 115 lines (8%) are > 80 characters long.
First few lines:
R/data.R#L17 #' @source \url{https://cf.10xgenomics.c ...
...
vignettes/introduction.Rmd#L123 toppSave(toppData, filename = "PBMC", sa ...
i NOTE: Consider multiples of 4 spaces for line indents; 61 lines (4%) are not.
First few lines:
R/topp_plot.R#L3 topp_results, ...
...
R/zzz.R#L6 for more information." ...
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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.47.1 results
0 ERRORS | 1 WARNINGS | i 9 NOTES
i See the scToppR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.