===============================
R CMD BUILD
===============================
* checking for file ‘partCNV/DESCRIPTION’ ... OK
* preparing ‘partCNV’:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘partCNV/data/Hg38_gtf.RData’ ‘partCNV/data/SimData.RData’
* building ‘partCNV_0.99.5.tar.gz’
===============================
BiocCheckGitClone('partCNV')
===============================
─ BiocCheckVersion: 1.35.19
─ BiocVersion: 3.17
─ Package: partCNV
─ PackageVersion: 0.99.5
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2861/c721e6e5ce29217c49492e317842d337bcd40cd2/partCNV
─ 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/2861/c721e6e5ce29217c49492e317842d337bcd40cd2/partCNV.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84269)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘partCNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘partCNV’ 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 ‘partCNV’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [18s/18s] 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 ... [38s/40s] NOTE
GetCytoLocation: no visible global function definition for ‘data’
GetExprCountCyto: no visible global function definition for ‘data’
Undefined global functions or variables:
data
Consider adding
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'GetExprCountCyto.Rd':
\examples lines wider than 100 characters:
GetExprCountCyto(cytoloc_output = res, Counts = as.matrix(SimData), normalization = TRUE, qt_cutoff = 0.99)
Rd file 'partCNV.Rd':
\examples lines wider than 100 characters:
exprout <- GetExprCountCyto(cytoloc_output = cytoloc, Counts = as.matrix(SimData), normalization = TRUE, qt_cutoff = 0.99)
Rd file 'partCNVH.Rd':
\examples lines wider than 100 characters:
exprout <- GetExprCountCyto(cytoloc_output = cytoloc, Counts = as.matrix(SimData), normalization = TRUE, qt_cutoff = 0.99)
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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [63s/67s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
partCNV 15.776 0.971 17.091
GetCytoLocation 9.559 1.437 13.426
partCNVH 7.415 0.676 8.407
GetExprCountCyto 4.348 0.921 5.591
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [67s/75s]
[67s/75s] 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 ... [3s/3s] OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2861/c721e6e5ce29217c49492e317842d337bcd40cd2/partCNV.Rcheck/00check.log’
for details.
===============================
BiocCheck('partCNV_0.99.5.tar.gz')
===============================
─ BiocCheckVersion: 1.35.19
─ BiocVersion: 3.17
─ Package: partCNV
─ PackageVersion: 0.99.5
─ sourceDir: /tmp/RtmpRIUl1W/file28888f7aeea48d/partCNV
─ installDir: /tmp/RtmpRIUl1W/file28888f54dbfbf8
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2861/c721e6e5ce29217c49492e317842d337bcd40cd2/partCNV.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...
* NOTE: Update R version dependency from 3.5.0 to 4.3.0.
* 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 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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’
* 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 partCNV...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 3 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* Checking package NEWS...
* 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; 115 lines (12%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 29 lines
(3%) 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 | 1 WARNINGS | 5 NOTES
See the partCNV.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.