Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘xenLite/DESCRIPTION’ ... OK
* preparing ‘xenLite’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘xenLite_0.99.2.tar.gz’

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 BiocCheckGitClone('xenLite')

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→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3542/d512e1a017ad039956a0b10a2f9cbbac89671e17/xenLite
→ BiocVersion: 3.20
→ Package: xenLite
→ PackageVersion: 0.99.2
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3542/d512e1a017ad039956a0b10a2f9cbbac89671e17/xenLite.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3542/d512e1a017ad039956a0b10a2f9cbbac89671e17/xenLite
→ 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 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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
  browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3542/d512e1a017ad039956a0b10a2f9cbbac89671e17/xenLite.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xenLite/DESCRIPTION’ ... OK
* this is package ‘xenLite’ version ‘0.99.2’
* 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 ‘xenLite’ 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] 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 ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [24s/24s] NOTE
e2sym: no visible binding for global variable ‘e79sym’
plot_xen_ggprep: no visible binding for global variable ‘vertex_x’
plot_xen_ggprep: no visible binding for global variable ‘vertex_y’
plot_xen_ggprep: no visible binding for global variable ‘cell_id’
plot_xen_ggprep: no visible binding for global variable ‘sizq’
Undefined global functions or variables:
  cell_id e79sym sizq vertex_x vertex_y

Found the following calls to data() loading into the global environment:
File ‘xenLite/R/e2sym.R’:
  data("e79sym", package = "xenLite")
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'cache_mtif.Rd':
  \usage lines wider than 90 characters:
         "https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenData/morphology_focus_0001.ome.tif"

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [53s/47s] OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
ggprep_seg      5.798  1.519   6.009
view_seg_g2     4.534  1.573   4.757
plot_xen_ggprep 4.097  1.454   4.370
view_seg        4.020  1.440   4.117
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [20s/18s]
 [21s/18s] 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: 2 NOTEs
See
  ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3542/d512e1a017ad039956a0b10a2f9cbbac89671e17/xenLite.Rcheck/00check.log’
for details.





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 BiocCheck('xenLite_0.99.2.tar.gz')

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── Installing xenLite ──────────────────────────────────────────────────────────
✔ Package installed successfully
── xenLite session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp8tjRtx/file3dbb330f5a41f/xenLite
→ BiocVersion: 3.20
→ Package: xenLite
→ PackageVersion: 0.99.2
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3542/d512e1a017ad039956a0b10a2f9cbbac89671e17/xenLite.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/Rtmp8tjRtx/file3dbb330f5a41f/xenLite
→ installDir: /tmp/Rtmp8tjRtx/file3dbb330c2bb28
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on xenLite ────────────────────────────────────────────────
* 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 4.1 to 4.4.0.
* 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 (47%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/xenLite.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of xenLite...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/view_seg_g.R (line 31, column 12)
• ...
• R/XenSPEP-class.R (line 86, column 11)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• XenSPEP-class.R (line 141, column 20)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/ggcode.R (line 7, column 3)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/cache_mtif.R (line 15, column 12)
• ...
• R/zipXenSPEP.R (line 44, column 7)
* 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 2
functions greater than 50 lines.
The longest 5 functions are:
• demoapp() (R/ebapp.R): 68 lines
• view_seg_g2() (R/view_seg_g.R): 59 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• loadGeometry.Rd
• reset_parq_paths.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...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 83 lines (8%) are > 80 characters long.
First few lines:
• R/cache_mtif.R#L10 #' if (!requireNamespace("tiff")) stop(" ...
• ...
• vignettes/xenLite.Rmd#L98 legend(5800,1390, fill=c("purple", "cyan ...
i NOTE: Consider multiples of 4 spaces for line indents; 234 lines (23%) are
not.
First few lines:
• R/cache_mtif.R#L16 url="https://mghp.osn.xsede.org/bir19 ...
• ...
• R/zipXenSPEP.R#L45 ans ...
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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 11 NOTES
i See the xenLite.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.