===============================
R CMD BUILD
===============================
* checking for file ‘PMScanR/DESCRIPTION’ ... OK
* preparing ‘PMScanR’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘PMScanR_0.99.0.tar.gz’
===============================
BiocCheckGitClone('PMScanR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3785/PMScanR_20250516212811/PMScanR
→ BiocVersion: 3.22
→ Package: PMScanR
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3785/PMScanR_20250516212811/PMScanR.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3785/PMScanR_20250516212811/PMScanR
→ 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 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 v1.45.7 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/3785/PMScanR_20250516212811/PMScanR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PMScanR/DESCRIPTION’ ... OK
* this is package ‘PMScanR’ version ‘0.99.0’
* 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 serialization versions ... OK
* checking whether package ‘PMScanR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 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 ... [8s/8s] NOTE
build_app: no visible global function definition for ‘shinyApp’
build_server: no visible global function definition for ‘observe’
build_server: no visible global function definition for ‘renderTable’
build_server: no visible global function definition for ‘renderPlotly’
Undefined global functions or variables:
observe renderPlotly renderTable shinyApp
* 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 files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] ERROR
Running examples in ‘PMScanR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runPsScan
> ### Title: Run PS-Scan
> ### Aliases: runPsScan
>
> ### ** Examples
>
> {
+ ps_scan <- "path/to/ps_scan.pl"
+ patterns_dat <- "path/to/prosite.dat"
+ out_format <- "fasta"
+ pf_scan <- "path/to/pfscan.exe"
+ out_file <- "out_Hb_fasta.txt"
+ in_file <- "hemoglobins.fasta"
+ runPsScan(in_file, out_file, out_format, ps_scan, patterns_dat, pf_scan, OS = "WIN")
+ }
Beggining of Prosite analysis
Error in shell(command) : could not find function "shell"
Calls: runPsScan -> execute_command
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
gff2matrix 8.221 0.364 8.586
* 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, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3785/PMScanR_20250516212811/PMScanR.Rcheck/00check.log’
for details.
===============================
BiocCheck('PMScanR_0.99.0.tar.gz')
===============================
── Installing PMScanR ──────────────────────────────────────────────────────────
✔ Package installed successfully
── PMScanR session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp39djOT/file266469212f0ee8/PMScanR
→ BiocVersion: 3.22
→ Package: PMScanR
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3785/PMScanR_20250516212811/PMScanR.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/Rtmp39djOT/file266469212f0ee8/PMScanR
→ installDir: /tmp/Rtmp39djOT/file26646949204e3b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on PMScanR ────────────────────────────────────────────────
* 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...
* 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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (7%).
* 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 .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 PMScanR...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• GetLogicalDrive.R (line 80, column 33)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/runPsScan.R (line 97, column 3)
• ...
• print() in R/server_PMScanR.R (line 153, column 7)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/runPsScan.R (line 157, column 15)
• R/runPsScan.R (line 189, column 17)
• R/runPsScan.R (line 221, column 15)
i NOTE: Avoid system() ; use system2()
Found in files:
• system() in R/GetLogicalDrive.R (line 46, column 30)
• system() in R/GetLogicalDrive.R (line 51, column 28)
• system() in R/runPsScan.R (line 262, column 5)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
• suppressWarnings() in R/read.prosite.R (line 125, column 21)
• ...
• suppressWarnings() in R/read.psa.R (line 89, column 16)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
The longest 5 functions are:
• build_server() (R/server_PMScanR.R): 313 lines
• ...
• getLogicalDrives() (R/GetLogicalDrive.R): 79 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• runPMScanRShiny.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 254 lines (13%) are > 80 characters long.
First few lines:
• R/app.R#L4 #' @return Launches the GUI for users no ...
• ...
• vignettes/PMScanR.Rmd#L280 Sigrist C.J.A., de Castro E., Cerutti L. ...
i NOTE: Consider multiples of 4 spaces for line indents; 636 lines (32%) are
not.
First few lines:
• R/app.R#L7 app <- build_app() ...
• ...
• vignettes/PMScanR.Rmd#L256 warning("Example PSA file path not fou ...
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 v1.45.7 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 13 NOTES
i See the PMScanR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.