===============================
R CMD BUILD
===============================
* checking for file igblastr/DESCRIPTION ... OK
* preparing igblastr:
* 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
* building igblastr_0.99.5.tar.gz
===============================
BiocCheckGitClone('igblastr')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3788/0bc7ed7f9e93b1b532c6468af96ddd05acb83184/igblastr
BiocVersion: 3.22
Package: igblastr
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3788/0bc7ed7f9e93b1b532c6468af96ddd05acb83184/igblastr.BiocCheck
BiocCheckVersion: 1.45.7
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3788/0bc7ed7f9e93b1b532c6468af96ddd05acb83184/igblastr
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
! WARNING: System files in '/inst' should not be Git tracked.
inst/extdata/ncbi_igblast_data_files/optional_file/human_gl.aux
...
inst/extdata/ncbi_igblast_data_files/optional_file/rhesus_monkey_gl.aux
* 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/3788/0bc7ed7f9e93b1b532c6468af96ddd05acb83184/igblastr.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 igblastr/DESCRIPTION ... OK
* this is package igblastr version 0.99.5
* 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 igblastr 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking whether startup messages can be suppressed ... [3s/3s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: jsonlite:::simplifyDataFrame
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] 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 ... [28s/25s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
igblastn 14.475 0.163 5.604
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [9s/12s]
[9s/12s] 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 ... [4s/4s] OK
* DONE
Status: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3788/0bc7ed7f9e93b1b532c6468af96ddd05acb83184/igblastr.Rcheck/00check.log
for details.
===============================
BiocCheck('igblastr_0.99.5.tar.gz')
===============================
Installing igblastr
Package installed successfully
igblastr session metadata
sourceDir: /tmp/RtmpjSEiHU/file27125319d9aaa5/igblastr
BiocVersion: 3.22
Package: igblastr
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3788/0bc7ed7f9e93b1b532c6468af96ddd05acb83184/igblastr.BiocCheck
BiocCheckVersion: 1.45.7
sourceDir: /tmp/RtmpjSEiHU/file27125319d9aaa5/igblastr
installDir: /tmp/RtmpjSEiHU/file27125322d7f861
isTarBall: TRUE
platform: unix
Running BiocCheck on igblastr
* 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 4.4.0 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...
i NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Alignment, SequenceMatching, DataImport
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 (25%).
* 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:
igblastr_overview.Rmd
! WARNING: Potential package installation calls found in vignette(s)
Found in files:
vignettes/igblastr_overview.Rmd (chunk no. 4, line 112, column 5)
vignettes/igblastr_overview.Rmd (chunk no. 9, line 181, column 1)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of igblastr...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
db-utils.R (line 24, column 15)
outfmt7-utils.R (line 320, column 64)
outfmt7-utils.R (line 322, column 63)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/db-utils.R (line 390, column 5)
print() in R/utils.R (line 317, column 5)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/auxiliary-data-utils.R (line 68, column 19)
...
R/igblastn.R (line 389, column 19)
! WARNING: .Deprecated / .Defunct usage (found 2 times)
.Deprecated() in R/long_to_wide_airr.R (line 12, column 5)
.Deprecated() in R/long_to_wide_airr.R (line 69, column 5)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 14 times)
suppressWarnings() in R/file-utils.R (line 137, column 19)
...
suppressWarnings() in R/utils.R (line 279, column 16)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 3
functions greater than 50 lines.
The longest 5 functions are:
igblastn() (R/igblastn.R): 73 lines
.copy_dir() (R/file-utils.R): 67 lines
long_to_wide_airr() (R/long_to_wide_airr.R): 56 lines
* Checking man page documentation...
* 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; 2 lines (0%) are > 80 characters long.
First few lines:
R/AIRR-utils.R#L11 ### https://wordpress.vdjbase.org/inde ...
vignettes/igblastr_overview.Rmd#L251 query <- system.file(package="igblastr",
...
i NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
First few lines:
R/cache-utils.R#L45 stop(wmsg("'which' must be one of ", ...
R/igblast_info.R#L77 .IGBLAST_VERSION_cache[[cmdpath]] <- ra ...
R/igblastn.R#L54 was_gz[[i]] <- TRUE ...
i NOTE: Consider multiples of 4 spaces for line indents; 850 lines (12%) are
not.
First few lines:
R/AIRR-utils.R#L85 release_version="published" ...
...
vignettes/igblastr_overview.Rmd#L388 Open Germline Reference Database. ...
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...
ERROR: Unable to find your email in the Support Site: HTTP 504 Gateway
Timeout.
BiocCheck v1.45.7 results
1 ERRORS | 2 WARNINGS | i 12 NOTES
i See the igblastr.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.