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R CMD BUILD
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* checking for file TrIdent/DESCRIPTION ... OK
* preparing TrIdent:
* 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 TrIdent_0.99.0.tar.gz
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BiocCheckGitClone('TrIdent')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3681/TrIdent_20241218172954/TrIdent
BiocVersion: 3.21
Package: TrIdent
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3681/TrIdent_20241218172954/TrIdent.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3681/TrIdent_20241218172954/TrIdent
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 v1.43.2 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3681/TrIdent_20241218172954/TrIdent.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 TrIdent/DESCRIPTION ... OK
* checking extension type ... Package
* this is package TrIdent 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 TrIdent 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 ... NOTE
Problems with news in NEWS.md:
No news entries found.
* 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 ... [1s/1s] 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 ... [7s/7s] 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 ... NOTE
Documented arguments not in \usage in Rd file 'prophageLikeBorders.Rd':
windowsize
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* 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 R/sysdata.rda ... OK
* checking files in vignettes ... OK
* checking examples ... [24s/24s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TrIdentClassifier 22.203 0.176 22.383
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [69s/69s]
[69s/69s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
1 1 4 3
3 of the prophage-like classifications are highly active or abundant
1 of the prophage-like classifications are mixed, i.e. heterogenously
integrated into their bacterial host population
2 contigs have potential specialized transduction
We recommend that you also view the results of this search with
logScale=TRUE
1 contigs have potential specialized transduction
We recommend that you also view the results of this search with
logScale=TRUE
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
Failed tests
Failure ('test-TrIdentClassifier.R:8:5'): default_TridentClassifer
`temp_tri_results` (`actual`) not equal to `TrIdentOutput` (`expected`).
`actual$PatternMatchInfo[[6]][[2]]`: 718.0
`expected$PatternMatchInfo[[6]][[2]]`: 729.1
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
Error: Test failures
Execution halted
* 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/3s] OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3681/TrIdent_20241218172954/TrIdent.Rcheck/00check.log
for details.
===============================
BiocCheck('TrIdent_0.99.0.tar.gz')
===============================
Installing TrIdent
Package installed successfully
TrIdent session metadata
sourceDir: /tmp/RtmpvIjBnn/file3ef4376432231f/TrIdent
BiocVersion: 3.21
Package: TrIdent
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3681/TrIdent_20241218172954/TrIdent.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpvIjBnn/file3ef4376432231f/TrIdent
installDir: /tmp/RtmpvIjBnn/file3ef43783b9340
isTarBall: TRUE
platform: unix
Running BiocCheck on TrIdent
* 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 4.2.0 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 TrIdent...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 52 times)
<<- in R/allPatternMatches.R (line 19, column 31)
...
<<- in R/VLPtoWCRatioCalc.R (line 38, column 27)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
The longest 5 functions are:
TrIdentClassifier() (R/TrIdentClassifier.R): 161 lines
...
patternMatcher() (R/patternMatcher.R): 108 lines
* 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 NOTE: Consider shorter lines; 12 lines (0%) are > 80 characters long.
First few lines:
R/NAremover.R#L6 #' \url{https://stackoverflow.com/questi ...
...
vignettes/TrIdent-vignette.Rmd#L445 ### NoPattern classifications with high
...
i NOTE: Consider multiples of 4 spaces for line indents; 114 lines (3%) are
not.
First few lines:
R/blockBuilder.R#L17 windowSize, ...
...
R/zeroCountSearch.R#L21 noReadCov) { ...
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 v1.43.2 results
0 ERRORS | 1 WARNINGS | i 5 NOTES
i See the TrIdent.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.