===============================
R CMD BUILD
===============================
* checking for file ‘Rarr/DESCRIPTION’ ... OK
* preparing ‘Rarr’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* running ‘cleanup’
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘Rarr_0.99.9.tar.gz’
===============================
BiocCheckGitClone('Rarr')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: Rarr
─ PackageVersion: 0.99.9
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2925/cc7d1b865c3b0f4529f0b366749018aa5f18f711/Rarr
─ 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/2925/cc7d1b865c3b0f4529f0b366749018aa5f18f711/Rarr.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* 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 ‘Rarr/DESCRIPTION’ ... OK
* this is package ‘Rarr’ version ‘0.99.9’
* 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:
inst/extdata/zarr_examples/column-first/boolean.zarr/.zarray
inst/extdata/zarr_examples/column-first/float16.zarr/.zarray
inst/extdata/zarr_examples/column-first/float32.zarr/.zarray
inst/extdata/zarr_examples/column-first/float64.zarr/.zarray
inst/extdata/zarr_examples/column-first/int16.zarr/.zarray
inst/extdata/zarr_examples/column-first/int32.zarr/.zarray
inst/extdata/zarr_examples/column-first/int64.zarr/.zarray
inst/extdata/zarr_examples/column-first/int8.zarr/.zarray
inst/extdata/zarr_examples/column-first/string.zarr/.zarray
inst/extdata/zarr_examples/column-first/uint16.zarr/.zarray
inst/extdata/zarr_examples/column-first/uint32.zarr/.zarray
inst/extdata/zarr_examples/column-first/uint64.zarr/.zarray
inst/extdata/zarr_examples/column-first/uint8.zarr/.zarray
inst/extdata/zarr_examples/compression/bzip2.zarr/.zarray
inst/extdata/zarr_examples/compression/lz4.zarr/.zarray
inst/extdata/zarr_examples/compression/lzma.zarr/.zarray
inst/extdata/zarr_examples/compression/zlib.zarr/.zarray
inst/extdata/zarr_examples/fill-values/double-inf.zarr/.zarray
inst/extdata/zarr_examples/fill-values/double-neginf.zarr/.zarray
inst/extdata/zarr_examples/row-first/float16.zarr/.zarray
inst/extdata/zarr_examples/row-first/float32.zarr/.zarray
inst/extdata/zarr_examples/row-first/float64.zarr/.zarray
inst/extdata/zarr_examples/row-first/int16.zarr/.zarray
inst/extdata/zarr_examples/row-first/int32.zarr/.zarray
inst/extdata/zarr_examples/row-first/int64.zarr/.zarray
inst/extdata/zarr_examples/row-first/int8.zarr/.zarray
inst/extdata/zarr_examples/row-first/string.zarr/.zarray
inst/extdata/zarr_examples/row-first/uint32.zarr/.zarray
inst/extdata/zarr_examples/row-first/uint64.zarr/.zarray
inst/extdata/zarr_examples/row-first/uint8.zarr/.zarray
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 serialization versions ... OK
* checking whether package ‘Rarr’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] 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] 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-mavx2’
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/302s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
zarr_overview 0.274 0.007 301.285
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.R’ [1s/1s]
[1s/1s] 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/2925/cc7d1b865c3b0f4529f0b366749018aa5f18f711/Rarr.Rcheck/00check.log’
for details.
===============================
BiocCheck('Rarr_0.99.9.tar.gz')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: Rarr
─ PackageVersion: 0.99.9
─ sourceDir: /tmp/Rtmp9fwk3o/file16ce5c63a1d0d0/Rarr
─ installDir: /tmp/Rtmp9fwk3o/file16ce5c7a5c528f
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2925/cc7d1b865c3b0f4529f0b366749018aa5f18f711/Rarr.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...
* 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 pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 Rarr...
* 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 2 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 6% of man pages use at least one of these tags.
* 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; 43 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 544 lines
(22%) 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 | 4 NOTES
See the Rarr.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.