===============================
R CMD BUILD
===============================
* checking for file ‘scToppR/DESCRIPTION’ ... OK
* preparing ‘scToppR’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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_0.99.1.tar.gz’
===============================
BiocCheckGitClone('scToppR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3523/8eb4c4e788b8137a2223287c398290046cde4780/scToppR
→ BiocVersion: 3.21
→ Package: scToppR
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3523/8eb4c4e788b8137a2223287c398290046cde4780/scToppR.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3523/8eb4c4e788b8137a2223287c398290046cde4780/scToppR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* 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 v1.43.2 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/3523/8eb4c4e788b8137a2223287c398290046cde4780/scToppR.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scToppR/DESCRIPTION’ ... OK
* this is package ‘scToppR’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ‘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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 ... [4s/4s] NOTE
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 ‘Cluster’
toppBalloon: no visible binding for global variable ‘geneRatio’
toppBalloon: no visible binding for global variable ‘Name’
toppBalloon: no visible binding for global variable ‘nlog10_fdr’
toppFun: no visible binding for global variable ‘genes_submit_cutoff’
toppPlot: no visible binding for global variable ‘Cluster’
toppPlot: no visible binding for global variable ‘Category’
toppPlot: no visible binding for global variable ‘GenesInTermInQuery’
toppPlot: no visible binding for global variable ‘GenesInTerm’
toppPlot: no visible binding for global variable ‘Name’
toppPlot: no visible binding for global variable ‘geneRatio’
toppSave: no visible binding for global variable ‘Cluster’
Undefined global functions or variables:
Category Cluster 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] INFO
Note: found 32 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/42s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
toppBalloon 6.887 0.105 6.992
toppFun 6.155 0.132 29.689
* 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3523/8eb4c4e788b8137a2223287c398290046cde4780/scToppR.Rcheck/00check.log’
for details.
===============================
BiocCheck('scToppR_0.99.1.tar.gz')
===============================
── Installing scToppR ──────────────────────────────────────────────────────────
✔ Package installed successfully
── scToppR session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpsIl3pL/file30c7c859746c54/scToppR
→ BiocVersion: 3.21
→ Package: scToppR
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3523/8eb4c4e788b8137a2223287c398290046cde4780/scToppR.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmpsIl3pL/file30c7c859746c54/scToppR
→ installDir: /tmp/RtmpsIl3pL/file30c7c824d5bf42
→ 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 4.3.0 to 4.5.0.
* 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 .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* 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 1:...; use seq_len() or seq_along()
Found in files:
• TOPP_GENE.R (line 215, column 45)
• TOPP_GENE.R (line 248, column 13)
• TOPP_GENE.R (line 273, column 13)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/TOPP_GENE.R (line 113, column 9)
• ...
• cat in R/topp_plot.R (line 256, column 21)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/TOPP_GENE.R (line 101, column 21)
• ...
• R/topp_plot.R (line 265, column 23)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/TOPP_GENE.R (line 71, column 10)
• R/topp_plot.R (line 53, column 12)
* 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:
• toppPlot() (R/topp_plot.R): 170 lines
• ...
• get_topp() (R/TOPP_GENE.R): 56 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 91 lines (8%) are > 80 characters long.
First few lines:
• R/data.R#L17 #' @source \url{https://cf.10xgenomics.c ...
• ...
• vignettes/introduction.Rmd#L83 scToppR will also automatically save the ...
i NOTE: Consider multiples of 4 spaces for line indents; 350 lines (30%) are
not.
First few lines:
• R/TOPP_GENE.R#L55 #Print message about the use of ToppGe ...
• ...
• vignettes/introduction.Rmd#L13 comment = "#>" ...
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 v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 9 NOTES
i See the scToppR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.