===============================
R CMD BUILD
===============================
* checking for file ‘vmrseq/DESCRIPTION’ ... OK
* preparing ‘vmrseq’:
* 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 ‘vmrseq_0.99.0.tar.gz’
===============================
BiocCheckGitClone('vmrseq')
===============================
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3455/vmrseq_20240716132005/vmrseq
─ BiocVersion: 3.20
─ Package: vmrseq
─ PackageVersion: 0.99.0
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3455/vmrseq_20240716132005/vmrseq.BiocCheck
─ BiocCheckVersion: 1.41.5
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3455/vmrseq_20240716132005/vmrseq
─ 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...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3455/vmrseq_20240716132005/vmrseq.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vmrseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘vmrseq’ version ‘0.99.0’
* 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘vmrseq’ 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
License stub is invalid DCF.
* 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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/28s] NOTE
.computeProb1Unit : .computeLag: no visible binding for global variable
‘chr’
.computeProb1Unit : .computeLag: no visible binding for global variable
‘state’
.computeProb1Unit : .computeLag: no visible binding for global variable
‘state_lag’
.computeProb1Unit : .computeLag: no visible binding for global variable
‘dist_bp’
.computeProb1Unit: no visible binding for global variable ‘dist_bp’
.computeProb1Unit: no visible binding for global variable ‘N_00’
.computeProb1Unit: no visible binding for global variable ‘N_10’
.computeProb1Unit: no visible binding for global variable ‘N_01’
.computeProb1Unit: no visible binding for global variable ‘N_11’
.computeProb1Unit: no visible binding for global variable ‘p_00’
.computeProb1Unit: no visible binding for global variable ‘p_01’
.estimTransitProbsFromSummary: no visible binding for global variable
‘dist_bp’
.estimTransitProbsFromSummary: no visible binding for global variable
‘p_00’
.estimTransitProbsFromSummary: no visible binding for global variable
‘p_01’
.estimTransitProbsFromSummary: no visible binding for global variable
‘p_10’
.estimTransitProbsFromSummary: no visible binding for global variable
‘p_11’
.estimTransitProbsFromSummary : .selectCols: no visible binding for
global variable ‘dist_bp’
HDF5NAdrop2matrix: no visible global function definition for ‘as’
computeVar : varByCluster: no visible global function definition for
‘as’
computeVarCutoff: no visible global function definition for ‘quantile’
extractInfo: no visible binding for global variable ‘meth’
extractInfo: no visible binding for global variable ‘total’
extractInfo: no visible binding for global variable ‘bool’
tp.plot: no visible binding for global variable ‘dist_bp’
tp.plot: no visible binding for global variable ‘pbar’
tp.plot: no visible binding for global variable ‘phat’
vmrseq.fit: no visible binding for global variable ‘bpWindow’
Undefined global functions or variables:
N_00 N_01 N_10 N_11 as bool bpWindow chr dist_bp meth p_00 p_01 p_10
p_11 pbar phat quantile state state_lag total
Consider adding
importFrom("methods", "as")
importFrom("stats", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'data.pool.Rd':
\examples lines wider than 100 characters:
## Not run: data.pool(cellFiles = your_cell_file_list, sep = ",", chrNames = "chr1", writeDir = "your/write/path")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [2s/2s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [65s/46s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
vmrseq.fit 19.474 0.940 11.538
vmrseq.smooth 18.495 1.645 11.187
* 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: 4 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3455/vmrseq_20240716132005/vmrseq.Rcheck/00check.log’
for details.
===============================
BiocCheck('vmrseq_0.99.0.tar.gz')
===============================
* Installing package...
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpZAzTKX/file11c2f64d0a8a3/vmrseq
─ BiocVersion: 3.20
─ Package: vmrseq
─ PackageVersion: 0.99.0
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3455/vmrseq_20240716132005/vmrseq.BiocCheck
─ BiocCheckVersion: 1.41.5
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpZAzTKX/file11c2f64d0a8a3/vmrseq
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpZAzTKX/file11c2f3eef990a
─ isTarBall: TRUE
─ platform: unix
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 3.5.0 to 4.4.0.
* 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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (50%).
* 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 vmrseq...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 12 functions greater than 50 lines.
* Checking man page documentation...
Registered S3 methods overwritten by 'proxy':
method from
print.registry_field registry
print.registry_entry registry
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 9% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* 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...
* NOTE: Consider shorter lines; 208 lines (9%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 694 lines
(31%) 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.
* ERROR: Add package to Watched Tags in your Support Site profile;
visit https://support.bioconductor.org/accounts/edit/profile
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 13 NOTES
See the vmrseq.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir vmrseq_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘vmrseq’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (vmrseq)