===============================
R CMD BUILD
===============================
* checking for file ‘stPipe/DESCRIPTION’ ... OK
* preparing ‘stPipe’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘stPipe_0.99.98.tar.gz’
===============================
BiocCheckGitClone('stPipe')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3720/7dc40c0913618f23c23de7e45d37f3b75dfffd3c/stPipe
→ BiocVersion: 3.22
→ Package: stPipe
→ PackageVersion: 0.99.98
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3720/7dc40c0913618f23c23de7e45d37f3b75dfffd3c/stPipe.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3720/7dc40c0913618f23c23de7e45d37f3b75dfffd3c/stPipe
→ 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/3720/7dc40c0913618f23c23de7e45d37f3b75dfffd3c/stPipe.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘stPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘stPipe’ version ‘0.99.98’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘stPipe’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 26.1Mb
sub-directories of 1Mb or more:
extdata 5.0Mb
libs 20.9Mb
* 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘SummarizedExperiment’
All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘stPipe_env’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [23s/23s] NOTE
Run_Create_Obj: no visible global function definition for ‘new’
Run_Create_Obj: no visible global function definition for ‘rowData<-’
Run_QC: no visible binding for global variable ‘Value’
Run_Visualization: no visible global function definition for ‘reorder’
Run_Visualization: no visible binding for global variable ‘status’
Run_Visualization: no visible binding for global variable ‘count’
Run_Visualization: no visible binding for global variable ‘percentage’
ref_pos: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
Value count new percentage read.csv reorder rowData<- status
Consider adding
importFrom("methods", "new")
importFrom("stats", "reorder")
importFrom("utils", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following assignments to the global environment:
File ‘stPipe/R/Run_Interactive.R’:
assign("selected_ROI", combined_selected_data, envir = .GlobalEnv)
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'Run_HTML.Rd':
\examples lines wider than 100 characters:
Spatial_Heatmap_of_UMI_Count_raw <- normalizePath(file.path(path, "Spatial_Heatmap_of_UMI_Count_raw.png"))
Spatial_Heatmap_of_UMI_Count_log <- normalizePath(file.path(path, "Spatial_Heatmap_of_UMI_Count_log.png"))
rmd_content <- gsub("<<Spatial_Heatmap_of_UMI_Count_raw>>", Spatial_Heatmap_of_UMI_Count_raw, rmd_content)
rmd_content <- gsub("<<Spatial_Heatmap_of_UMI_Count_log>>", Spatial_Heatmap_of_UMI_Count_log, rmd_content)
These lines will be truncated in the PDF manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/pkgbuild/packagebuilder/workers/jobs/3720/R-libs/stPipe/libs/stPipe.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘rand_r’, possibly from ‘rand_r’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... [181s/183s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Run_ST 147.445 20.364 169.866
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [13s/13s]
[13s/13s] OK
* 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 WARNING, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3720/7dc40c0913618f23c23de7e45d37f3b75dfffd3c/stPipe.Rcheck/00check.log’
for details.
===============================
BiocCheck('stPipe_0.99.98.tar.gz')
===============================
── Installing stPipe ───────────────────────────────────────────────────────────
✔ Package installed successfully
── stPipe session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp9r4dxS/file24ea506ee56bef/stPipe
→ BiocVersion: 3.22
→ Package: stPipe
→ PackageVersion: 0.99.98
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3720/7dc40c0913618f23c23de7e45d37f3b75dfffd3c/stPipe.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/Rtmp9r4dxS/file24ea506ee56bef/stPipe
→ installDir: /tmp/Rtmp9r4dxS/file24ea504c16d0a9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on stPipe ─────────────────────────────────────────────────
* 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...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (35%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• stPipe-vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of stPipe...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• data.R (line 59, column 56)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/Run_ST.R (line 163, column 14)
i NOTE: Avoid system() ; use system2()
Found in files:
• system() in R/Run_Loc_Match.R (line 125, column 5)
• system() in R/Run_ST.R (line 160, column 9)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
• suppressWarnings() in R/Run_QC.R (line 123, column 3)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
The longest 5 functions are:
• Run_ST() (R/Run_ST.R): 246 lines
• ...
• Run_Visualization() (R/Run_Visualization.R): 100 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• Run_Create_Obj.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; 253 lines (13%) are > 80 characters long.
First few lines:
• R/data.R#L3 #' A pair of gzipped FASTQ files for dem ...
• ...
• vignettes/stPipe-vignette.Rmd#L197 Upstream pre-processing is never the end
...
i NOTE: Consider multiples of 4 spaces for line indents; 525 lines (27%) are
not.
First few lines:
• R/basilisk.R#L3 envname = "stPipe_env", ...
• ...
• vignettes/stPipe-vignette.Rmd#L207 ) ...
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 v1.45.7 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 9 NOTES
i See the stPipe.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.