===============================
R CMD BUILD
===============================
* checking for file TaxSEA/DESCRIPTION ... OK
* preparing TaxSEA:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
TaxSEA/data/NCBI_ids.rda TaxSEA/data/TaxSEA_db.rda
TaxSEA/data/TaxSEA_test_data.rda
* building TaxSEA_0.99.0.tar.gz
===============================
BiocCheckGitClone('TaxSEA')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3627/TaxSEA_20241122195422/TaxSEA
BiocVersion: 3.21
Package: TaxSEA
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3627/TaxSEA_20241122195422/TaxSEA.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3627/TaxSEA_20241122195422/TaxSEA
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
TaxSEA.Rproj
* 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 v1.43.2 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/3627/TaxSEA_20241122195422/TaxSEA.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* 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 TaxSEA/DESCRIPTION ... OK
* checking extension type ... Package
* this is package TaxSEA version 0.99.0
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 TaxSEA 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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] INFO
Note: found 29 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [1s/1s] 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: OK
===============================
BiocCheck('TaxSEA_0.99.0.tar.gz')
===============================
Installing TaxSEA
Package installed successfully
TaxSEA session metadata
sourceDir: /tmp/Rtmp1gn6jI/file3cd26a3c9ff241/TaxSEA
BiocVersion: 3.21
Package: TaxSEA
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3627/TaxSEA_20241122195422/TaxSEA.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/Rtmp1gn6jI/file3cd26a3c9ff241/TaxSEA
installDir: /tmp/Rtmp1gn6jI/file3cd26a3ec66f34
isTarBall: TRUE
platform: unix
Running BiocCheck on TaxSEA
* 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 3.5.0 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...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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 TaxSEA...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/get_taxon_sets.R (line 17, column 9)
R/TaxSEA.R (line 132, column 23)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/TaxSEA.R (line 84, column 13)
* 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:
TaxSEA() (R/TaxSEA.R): 100 lines
TaxSEA_barplot() (R/plotting.R): 52 lines
* Checking man page documentation...
* 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; 3 lines (1%) are > 80 characters long.
First few lines:
vignettes/my-vignette.Rmd#L105 x = "d__Bacteria.p__Actinobacteriota.c__ ...
vignettes/my-vignette.Rmd#L110 #new_ids = sapply(as.character(old_ids), ...
vignettes/my-vignette.Rmd#L164 #E.g. if the BugSigDB identifier you fou ...
i NOTE: Consider multiples of 4 spaces for line indents; 125 lines (21%) are
not.
First few lines:
R/get_NCBI_sets.R#L14 get_ncbi_taxon_id <- function(taxon_na ...
...
vignettes/my-vignette.Rmd#L168 bsdb$Signature=="Signature 2",] ...
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...
ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.43.2 results
1 ERRORS | 1 WARNINGS | i 7 NOTES
i See the TaxSEA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.