===============================
R CMD BUILD
===============================
* checking for file sfi/DESCRIPTION ... OK
* preparing sfi:
* 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
* looking to see if a data/datalist file should be added
* building sfi_0.99.0.tar.gz
===============================
BiocCheckGitClone('sfi')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3876/sfi_20250904150825/sfi
BiocVersion: 3.22
Package: sfi
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3876/sfi_20250904150825/sfi.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3876/sfi_20250904150825/sfi
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
sfi.Rproj
* 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 v1.45.18 results
1 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/3876/sfi_20250904150825/sfi.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 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file sfi/DESCRIPTION ... OK
* checking extension type ... Package
* this is package sfi 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 whether package sfi can be installed ... WARNING
Found the following significant warnings:
sfi.cpp:11:7: warning: Grid2D::mz_bins will be initialized after [-Wreorder]
sfi.cpp:10:10: warning: double Grid2D::mz_min [-Wreorder]
sfi.cpp:13:3: warning: when initialized here [-Wreorder]
sfi.cpp:11:16: warning: Grid2D::rt_bins will be initialized after [-Wreorder]
sfi.cpp:10:26: warning: double Grid2D::rt_min [-Wreorder]
sfi.cpp:10:34: warning: Grid2D::rt_max will be initialized after [-Wreorder]
sfi.cpp:8:24: warning: const Rcpp::NumericVector& Grid2D::mz_values [-Wreorder]
See /home/pkgbuild/packagebuilder/workers/jobs/3876/sfi_20250904150825/sfi.Rcheck/00install.out for details.
* used C++ compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] OK
* 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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 ... NOTE
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [159s/157s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getsff 110.451 11.444 121.920
getqc 13.256 1.374 14.485
getwindow 8.774 0.758 9.533
getsfm 7.630 0.013 5.376
* 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, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3876/sfi_20250904150825/sfi.Rcheck/00check.log
for details.
===============================
BiocCheck('sfi_0.99.0.tar.gz')
===============================
Installing sfi
Package installed successfully
sfi session metadata
sourceDir: /tmp/RtmprNSG6U/file3b9da4d329748/sfi
BiocVersion: 3.22
Package: sfi
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3876/sfi_20250904150825/sfi.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /tmp/RtmprNSG6U/file3b9da4d329748/sfi
installDir: /tmp/RtmprNSG6U/file3b9da38cc0d3b
isTarBall: TRUE
platform: unix
Running BiocCheck on sfi
* 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...
i NOTE: Consider adding these automatically suggested biocViews:
QualityControl, FeatureExtraction
i Search 'biocViews' at https://contributions.bioconductor.org
* 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 (20%).
* 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:
workflow.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of sfi...
* Checking coding practice...
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/sfi.R (line 173, column 11)
...
R/sfi.R (line 793, column 11)
* 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 5
functions greater than 50 lines.
The longest 5 functions are:
getsfm() (R/sfi.R): 192 lines
...
getsff() (R/sfi.R): 75 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
getmzml.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
Found in files:
getmzml.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
getmzml.Rd
* 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; 56 lines (6%) are > 80 characters long.
First few lines:
R/RcppExports.R#L4 find_2d_peaks_c <- function(mz, rt, inte ...
...
vignettes/workflow.Rmd#L120 ndf <- getsfm(mz,rt,intensity,idelta=ide ...
i NOTE: Consider multiples of 4 spaces for line indents; 428 lines (43%) are
not.
First few lines:
R/sfi.R#L19 mzml_file <- mzR::openMSfile(path) ...
...
vignettes/workflow.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 v1.45.18 results
0 ERRORS | 0 WARNINGS | i 11 NOTES
i See the sfi.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.