===============================
BiocCheckGitClone('ClusterFoldSimilarity')
===============================
─ BiocCheckVersion: 1.37.9
─ BiocVersion: 3.18
─ Package: ClusterFoldSimilarity
─ PackageVersion: 0.99.6
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2900/7cd5fb8d60189d56d72151f945d95a9f01c89d24/ClusterFoldSimilarity
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2900/7cd5fb8d60189d56d72151f945d95a9f01c89d24/ClusterFoldSimilarity.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClusterFoldSimilarity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClusterFoldSimilarity’ version ‘0.99.6’
* 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 serialization versions ... OK
* checking whether package ‘ClusterFoldSimilarity’ 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... [4s/4s] NOTE
similarityHeatmap: no visible binding for global variable ‘clusterL’
similarityHeatmap: no visible binding for global variable ‘clusterR’
similarityHeatmap: no visible binding for global variable
‘similarityValue’
Undefined global functions or variables:
clusterL clusterR similarityValue
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'clusterFoldSimilarity.Rd':
\examples lines wider than 100 characters:
colData <- data.frame(cluster=sample(c("Cluster1","Cluster2","Cluster3"),size = ncells,replace = TRUE),
colData <- data.frame(cluster=sample(c("Cluster1","Cluster2","Cluster3","Cluster4"),size = ncells,replace = TRUE),
similarity.table <- clusterFoldSimilarity(sceList = singlecell.object.list, sampleNames = c("sc1","sc2"))
Rd file 'plotClustersGraph.Rd':
\examples lines wider than 100 characters:
colData <- data.frame(cluster=sample(c("Cluster1","Cluster2","Cluster3"),size = ncells,replace = TRUE),
colData <- data.frame(cluster=sample(c("Cluster1","Cluster2","Cluster3","Cluster4"),size = ncells,replace = TRUE),
similarity.table <- clusterFoldSimilarity(sceList = singlecell.object.list, sampleNames = c("sc1","sc2"))
Rd file 'similarityHeatmap.Rd':
\examples lines wider than 100 characters:
colData <- data.frame(cluster=sample(c("Cluster1","Cluster2","Cluster3"),size = ncells,replace = TRUE),
colData <- data.frame(cluster=sample(c("Cluster1","Cluster2","Cluster3","Cluster4"),size = ncells,replace = TRUE),
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 files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [2s/2s] OK
* DONE
Status: 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2900/7cd5fb8d60189d56d72151f945d95a9f01c89d24/ClusterFoldSimilarity.Rcheck/00check.log’
for details.
===============================
BiocCheck('ClusterFoldSimilarity_0.99.6.tar.gz')
===============================
─ BiocCheckVersion: 1.37.9
─ BiocVersion: 3.18
─ Package: ClusterFoldSimilarity
─ PackageVersion: 0.99.6
─ sourceDir: /tmp/RtmpqCuRwK/file29d0e15835d62b/ClusterFoldSimilarity
─ installDir: /tmp/RtmpqCuRwK/file29d0e16cb5d236
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2900/7cd5fb8d60189d56d72151f945d95a9f01c89d24/ClusterFoldSimilarity.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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...
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
RNASeq
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import graphics, stats, utils in DESCRIPTION as well as
NAMESPACE.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ClusterFoldSimilarity...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
Found @ in vignettes/ClusterFoldSimilarity.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 4 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* 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...
* NOTE: Consider shorter lines; 244 lines (22%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 230 lines
(21%) are not.
See https://contributions.bioconductor.org/r-code.html
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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 2 WARNINGS | 14 NOTES
See the ClusterFoldSimilarity.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.