===============================
BiocCheckGitClone('stPipe')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3720/ca9f7a73fec60abb16b5da185e6121edc59ee448/stPipe
BiocVersion: 3.22
Package: stPipe
PackageVersion: 0.99.91
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3720/ca9f7a73fec60abb16b5da185e6121edc59ee448/stPipe.BiocCheck
BiocCheckVersion: 1.45.7
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3720/ca9f7a73fec60abb16b5da185e6121edc59ee448/stPipe
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
! WARNING: System files in '/inst' should not be Git tracked.
inst/.DS_Store
...
inst/rmarkdown/templates/stpipe-report/.DS_Store
* 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 | 1 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3720/ca9f7a73fec60abb16b5da185e6121edc59ee448/stPipe.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 stPipe/DESCRIPTION ... OK
* checking extension type ... Package
* this is package stPipe version 0.99.91
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 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 26.2Mb
sub-directories of 1Mb or more:
extdata 5.0Mb
libs 21.0Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking build directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
rmarkdown shiny umap
A package should be listed in only one of these fields.
* 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 ... WARNING
'::' or ':::' import not declared from: basilisk
Namespaces in Imports field not imported from:
AnnotationDbi RcppArmadillo Rhdf5lib curl irlba
org.Hs.eg.db parallel patchwork rhdf5 scales viridis
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_Clustering: no visible binding for global variable TSNE1
Run_Clustering: no visible binding for global variable TSNE2
Run_Clustering: no visible binding for global variable cluster
Run_Clustering: no visible binding for global variable UMAP1
Run_Clustering: no visible binding for global variable UMAP2
Run_Create_Obj: no visible global function definition for new
Run_Create_Obj: no visible global function definition for rowData<-
Run_HTML: no visible global function definition for read.csv
Run_Interactive: no visible binding for global variable X_coordinate
Run_Interactive: no visible binding for global variable Y_coordinate
Run_Interactive: no visible binding for global variable UMI_count
Run_Interactive: no visible binding for global variable spatial_name
Run_Interactive: no visible binding for global variable TSNE1
Run_Interactive: no visible binding for global variable TSNE2
Run_Interactive: no visible binding for global variable cluster
Run_Interactive: no visible binding for global variable UMAP1
Run_Interactive: no visible binding for global variable UMAP2
Run_Interactive : <anonymous>: no visible binding for global variable
spatial_name
Run_Loc_Match: no visible global function definition for head
Run_Loc_Match: no visible global function definition for read.csv
Run_Loc_Match: no visible global function definition for
complete.cases
Run_QC: no visible binding for global variable Percentile
Run_QC: no visible binding for global variable Value
Run_Visualization: no visible binding for global variable
X_coordinate
Run_Visualization: no visible binding for global variable
Y_coordinate
Run_Visualization: no visible binding for global variable UMI_count
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
Undefined global functions or variables:
Percentile TSNE1 TSNE2 UMAP1 UMAP2 UMI_count Value X_coordinate
Y_coordinate cluster complete.cases count head new percentage
read.csv reorder rowData<- spatial_name status
Consider adding
importFrom("methods", "new")
importFrom("stats", "complete.cases", "reorder")
importFrom("utils", "head", "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 ... WARNING
Undocumented code objects:
RunDemultiplex
All user-level objects in a package should have documentation entries.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section Writing portable
packages in the Writing R Extensions manual.
* 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 _ZSt4cout, possibly from std::cout (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 ... [178s/180s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Run_ST 144.631 20.505 167.189
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [9s/9s]
[9s/9s] 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: 4 WARNINGs, 4 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3720/ca9f7a73fec60abb16b5da185e6121edc59ee448/stPipe.Rcheck/00check.log
for details.
===============================
BiocCheck('stPipe_0.99.91.tar.gz')
===============================
Installing stPipe
Package installed successfully
stPipe session metadata
sourceDir: /tmp/RtmpbikpHs/file3de94c34896735/stPipe
BiocVersion: 3.22
Package: stPipe
PackageVersion: 0.99.91
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3720/ca9f7a73fec60abb16b5da185e6121edc59ee448/stPipe.BiocCheck
BiocCheckVersion: 1.45.7
sourceDir: /tmp/RtmpbikpHs/file3de94c34896735/stPipe
installDir: /tmp/RtmpbikpHs/file3de94c7af01b7c
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...
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...
i Bioconductor dependencies found in Imports & Depends (28%).
* 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 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 120, 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; 243 lines (14%) are > 80 characters long.
First few lines:
R/help.R#L1 #' stPipe: A package for pre-processing ...
...
vignettes/stPipe-vignette.Rmd#L197 Upstream pre-processing is never the end
...
i NOTE: Consider multiples of 4 spaces for line indents; 510 lines (30%) 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.