===============================
R CMD BUILD
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* checking for file poem/DESCRIPTION ... OK
* preparing poem:
* 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 poem_0.99.2.tar.gz
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BiocCheckGitClone('poem')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3618/poem_20241204194450/poem
BiocVersion: 3.21
Package: poem
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3618/poem_20241204194450/poem.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3618/poem_20241204194450/poem
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
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3618/poem_20241204194450/poem.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 poem/DESCRIPTION ... OK
* this is package poem version 0.99.2
* 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 poem 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 ... [7s/7s] 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 ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [27s/27s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'getFuzzyPartitionMetrics.Rd':
\examples lines wider than 100 characters:
getFuzzyPartitionMetrics(hardPred=hardPred, hardTrue=hardTrue, fuzzyTrue=fuzzyTrue, nperms=3, level="class")
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... NOTE
Unknown packages FuzzyPartitionMetrics(), fuzzyHardMetrics() in Rd xrefs
* 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 2 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [16s/16s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [9s/9s]
[9s/9s] 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: 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3618/poem_20241204194450/poem.Rcheck/00check.log
for details.
===============================
BiocCheck('poem_0.99.2.tar.gz')
===============================
Installing poem
Package installed successfully
poem session metadata
sourceDir: /tmp/RtmpORzPbf/file3aa98019eede24/poem
BiocVersion: 3.21
Package: poem
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3618/poem_20241204194450/poem.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpORzPbf/file3aa98019eede24/poem
installDir: /tmp/RtmpORzPbf/file3aa9802fbc609e
isTarBall: TRUE
platform: unix
Running BiocCheck on poem
* 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 4.0 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: ATACSeq
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 (18%).
* 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 poem...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/fuzzyPartitionMetrics.R (line 116, column 10)
...
R/SpatialMetrics.R (line 27, column 9)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
fuzzyPartitionMetrics.R (line 157, column 22)
...
fuzzyPartitionMetrics.R (line 582, column 21)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/CDbw.R (line 144, column 5)
...
print() in R/CDbw.R (line 181, column 5)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/fuzzyPartitionMetrics.R (line 320, column 15)
...
R/getFuzzyPartitionMetrics.R (line 95, column 15)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/fuzzyPartitionMetrics.R (line 179, column 13)
R/fuzzyPartitionMetrics.R (line 403, column 13)
R/fuzzyPartitionMetrics.R (line 591, column 13)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
suppressWarnings() in R/simulation.R (line 50, column 14)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
The longest 5 functions are:
CDbw() (R/CDbw.R): 146 lines
...
getPartitionClassMetrics() (R/getPartitionClassMetrics.R): 113 lines
* Checking man page documentation...
Registered S3 method overwritten by 'e1071':
method from
print.fclust fclust
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
matchSets.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; 308 lines (7%) are > 80 characters long.
First few lines:
R/CDbw.R#L30 #' approach using multi-representatives. ...
...
vignettes/table.rmd#L168 styled_kable_table <- kableExtra::kable_ ...
i NOTE: Consider multiples of 4 spaces for line indents; 1758 lines (37%) are
not.
First few lines:
R/CDbw.R#L41 clusterstdev=TRUE, trac ...
...
vignettes/table.rmd#L160 stringsAsFactors = FALSE ...
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.
ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
BiocCheck v1.43.2 results
2 ERRORS | 0 WARNINGS | i 13 NOTES
i See the poem.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.