===============================
R CMD BUILD
===============================
* checking for file ‘SpectraQL/DESCRIPTION’ ... OK
* preparing ‘SpectraQL’:
* 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
WARNING: directory ‘SpectraQL/man/figures’ is empty
Omitted ‘LazyData’ from DESCRIPTION
* building ‘SpectraQL_0.99.1.tar.gz’
===============================
BiocCheckGitClone('SpectraQL')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3525/9eb4fc63017ce73555df13b2050f887e4fa9fb5b/SpectraQL
→ BiocVersion: 3.20
→ Package: SpectraQL
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3525/9eb4fc63017ce73555df13b2050f887e4fa9fb5b/SpectraQL.BiocCheck
→ BiocCheckVersion: 1.41.16
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3525/9eb4fc63017ce73555df13b2050f887e4fa9fb5b/SpectraQL
→ 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 N: (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 v1.41.16 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3525/9eb4fc63017ce73555df13b2050f887e4fa9fb5b/SpectraQL.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpectraQL/DESCRIPTION’ ... OK
* this is package ‘SpectraQL’ version ‘0.99.1’
* 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 ‘SpectraQL’ 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 ... 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [10s/10s] 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 files in ‘vignettes’ ... OK
* checking examples ... [11s/10s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
query 5.863 1.268 6.957
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [11s/11s]
[11s/11s] 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 ... [2s/2s] OK
* DONE
Status: OK
===============================
BiocCheck('SpectraQL_0.99.1.tar.gz')
===============================
── Installing SpectraQL ────────────────────────────────────────────────────────
✔ Package installed successfully
── SpectraQL session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAoCJkT/file18777c3371ca69/SpectraQL
→ BiocVersion: 3.20
→ Package: SpectraQL
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3525/9eb4fc63017ce73555df13b2050f887e4fa9fb5b/SpectraQL.BiocCheck
→ BiocCheckVersion: 1.41.16
→ sourceDir: /tmp/RtmpAoCJkT/file18777c3371ca69/SpectraQL
→ installDir: /tmp/RtmpAoCJkT/file18777c69b3b7c7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SpectraQL ──────────────────────────────────────────────
* 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 (75%).
* 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 SpectraQL...
* Checking coding practice...
i N: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/massql-parser.R (line 63, column 14)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* 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 N: Consider shorter lines; 2 lines (0%) are > 80 characters long.
First few lines:
• vignettes/SpectraQL.Rmd#L57 (e.g. [MsBackendMassbank](https://rforma ...
• vignettes/SpectraQL.Rmd#L77 [definition](https://mwang87.github.io/M ...
i N: Consider multiples of 4 spaces for line indents; 30 lines (3%) are not.
First few lines:
• R/massql-parser.R#L33 label = "C ...
• ...
• vignettes/SpectraQL.Rmd#L312 " filter ms1mz = 219.095:tole ...
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 v1.41.16 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 3 NOTES
i See the SpectraQL.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.